shigej38 commented 5 years ago

Hello Offical: Is there a plugin or parameter that can print out diseases caused by genes?

at7 commented 5 years ago

Hi @shigej38, we have categorised our VEP plugins here. You will probably find the Phenotype plugin useful. Please find more documentation in the Phenotypes plugin description. Best reagards, Anja

shigej38 commented 5 years ago

do I access the "gff" file needed for a phenotype plugin?

at7 commented 5 years ago

On the first run the plugin will download a GFF file to ~/.vep/Plugins/. After that you can specify the location of the GFF file with --plugin Phenotypes,file=/path/to/phenotypes.gff.gz. This is all described in the documentation of the plugin: https://github.com/Ensembl/VEP_plugins/blob/release/97/Phenotypes.pm

shigej38 commented 5 years ago

I used command: ./vep --plugin Phenotypes --database --refseq --port 3337 --format vcf

error output: `### Phenotypes plugin: Generating GFF file /home/detagen/.vep/Plugins/Phenotypes.pm_homo_sapiens_97_GRCh37.gvf.gz from database

Phenotypes plugin: This will take some time but it will only run once per species, assembly and release

Phenotypes plugin: Querying database

Phenotypes plugin: Writing to file

Phenotypes plugin: Sorting file with sort

Phenotypes plugin: Indexing file with tabix

[E::get_intv] Failed to parse TBX_GENERIC, was wrong -p [type] used? The offending line was: "Binary file (standard input) matches" [E::hts_idx_push] Unsorted positions on sequence #22: 141073853 followed by 0 tbx_index_build failed: /home/detagen/.vep/Plugins/Phenotypes.pm_homo_sapiens_97_GRCh37.gvf.gz WARNING: Failed to instantiate plugin Phenotypes: ERROR: tabix failed`

at7 commented 5 years ago

Dear @shigej38, I'm not able to reproduce the error. Could you please check the file size of /home/detagen/.vep/Plugins/Phenotypes.pm_homo_sapiens_97_GRCh37.gvf.gz? And could you please try to generate the tabix file manually by running cd /home/detagen/.vep/Plugins/ tabix -p gff Phenotypes.pm_homo_sapiens_97_GRCh37.gvf.gz? Thank you, Anja

shigej38 commented 5 years ago

the size of my file is 73.4 MB "Phenotypes.pm_homo_sapiens_97_GRCh37.gvf.gz"

tabix -p gff Phenotypes.pm_homo_sapiens_97_GRCh37.gvf.gz

[E::get_intv] Failed to parse TBX_GENERIC, was wrong -p [type] used? The offending line was: "Binary file (standard input) matches" [E::hts_idx_push] Unsorted positions on sequence #22: 141073853 followed by 0 tbx_index_build failed: Phenotypes.pm_homo_sapiens_97_GRCh37.gvf.gz

at7 commented 5 years ago

I just realised that we had the same error already reported by someone else (https://github.com/Ensembl/ensembl-vep/issues/579). I merged the fix into the release/97 branch. Could you please get the latest checkout, delete the Phenotypes.pm_homo_sapiens_97_GRCh37.gvf.gz file and rerun VEP with the Phenotypes plugin? Thank you, Anja

shigej38 commented 5 years ago

my used commands:

git pull ` remote: Enumerating objects: 34, done.

remote: Counting objects: 100% (34/34), done.

remote: Compressing objects: 100% (13/13), done.

remote: Total 34 (delta 12), reused 22 (delta 9), pack-reused 0

Unpacking objects: 100% (34/34), done.

From https://github.com/Ensembl/ensembl-vep

948645b..a3b6d64 master -> origin/master

b20aea7..d788dfd postreleasefix/98 -> origin/postreleasefix/98

a277392..6e3367f release/98 -> origin/release/98

Already up to date. `

git checkout release/97 Already on 'release/97' Your branch is up to date with 'origin/release/97'.

output: `./vep --plugin Phenotypes --database --refseq --port 3337 --format vcf

Phenotypes plugin: Generating GFF file /home/detagen/.vep/Plugins/Phenotypes.pm_homo_sapiens_97_GRCh37.gvf.gz from database

Phenotypes plugin: This will take some time but it will only run once per species, assembly and release

Phenotypes plugin: Querying database

Phenotypes plugin: Writing to file

Phenotypes plugin: Sorting file with sort

Phenotypes plugin: Indexing file with tabix

[E::get_intv] Failed to parse TBX_GENERIC, was wrong -p [type] used? The offending line was: "Binary file (standard input) matches" [E::hts_idx_push] Unsorted positions on sequence #22: 141073853 followed by 0 tbx_index_build failed: /home/detagen/.vep/Plugins/Phenotypes.pm_homo_sapiens_97_GRCh37.gvf.gz WARNING: Failed to instantiate plugin Phenotypes: ERROR: tabix failed `

ım trying manual indexing: tabix -p gff Phenotypes.pm_homo_sapiens_97_GRCh37.gvf.gz [E::get_intv] Failed to parse TBX_GENERIC, was wrong -p [type] used? The offending line was: "Binary file (standard input) matches" [E::hts_idx_push] Unsorted positions on sequence #22: 141073853 followed by 0 tbx_index_build failed: Phenotypes.pm_homo_sapiens_97_GRCh37.gvf.gz

and again trying manual indexing tmp file: tabix -p gff Phenotypes.pm_homo_sapiens_97_GRCh37.gvf.gz.tmp [E::hts_idx_push] Unsorted positions on sequence #3: 2354033 followed by 2353674 tbx_index_build failed: Phenotypes.pm_homo_sapiens_97_GRCh37.gvf.gz.tmp

at7 commented 5 years ago

Dear @shigej38, I'm sorry I wasn't clear enough. But you need to refresh the Phenotype.pm file which is under https://github.com/Ensembl/VEP_plugins. The best way is to fetch the latest changes for https://github.com/Ensembl/VEP_plugins for the release/97 branch and then copy Phenotype.pm into your plugins directory. Thank you, Anja

shigej38 commented 5 years ago

The indexing problem of the file is solved when you update the Phenotypes.pm file. however, when I use the --fields parameter ( ı used PHENOTYPES), when I refer to line 178 of Phenotypes.pm, the entire column is empty (-). I think it's a problem like 231 (https://github.com/Ensembl/VEP_plugins/issues/231#issuecomment-523514191) . What string should I write in fields for phenotypes?

my used command is: /home/detagen/Desktop/programlar/ensembl-vep/vep --fork 1 --refseq --use_given_ref --force_overwrite --coding_only -i /home/detagen/Desktop/result/input/FMF-248.vcf -o /home/detagen/Desktop/result/output/FMF-248.csv --cache --offline --assembly GRCh37 --tab --check_existing --biotype --canonical --domains --uniprot --ccds --symbol --protein --hgvs --no_escape --numbers --show_ref_allele --allele_number --individual all --regulatory --humdiv --polyphen p --sift p --variant_class --plugin dbNSFP,/home/detagen/Desktop/programlar/ensembl-data/dbNSFP3.5/dbNSFP3.5.gz,ALL --plugin Condel,/home/detagen/.vep/Plugins/config/Condel/config/condel_SP.conf,p --fasta /home/detagen/Desktop/programlar/ensembl-data/fasta/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa --plugin Mastermind,/home/detagen/Desktop/programlar/ensembl-data/mastermind/mastermind_cited_variants_reference-2019.06.14-grch37.vcf.gz --plugin G2P,file=/home/detagen/Desktop/programlar/ensembl-data/G2P/DDG2P_10_7_2019.csv,log_dir=/home/detagen/Desktop/result/log/FMF-248.vcf,txt_report=/home/detagen/Desktop/result/log/FMF-248.vcf/FMF-248.txt,html_report=/home/detagen/Desktop/result/log/FMF-248.vcf/FMF-248.html --fields 'Uploaded_variation,PHENOTYPES,cDNA_position,REF_ALLELE,Allele,Protein_position,Amino_acids,Codons,SYMBOL,EXON,INTRON,ZYG,Consequence,CLIN_SIG,Existing_variation,rs_dbSNP150,G2P_complete,G2P_flag,G2P_gene_req,Mastermind_MMID3,Mastermind_counts,clinvar_rs,clinvar_trait,DOMAINS,Interpro_domain,hg18_chr,hg18_pos(1-based),hg19_chr,hg19_pos(1-based),ExAC_AC,ExAC_AF,gnomAD_exomes_AC,gnomAD_exomes_AF,gnomAD_genomes_AC,gnomAD_genomes_AF,Ensembl_geneid,Ensembl_proteinid,Ensembl_transcriptid,HGVSc,HGVSp,Location,Gene,Feature,Feature_type,CDS_position,IND,ALLELE_NUM,IMPACT,DISTANCE,STRAND,FLAGS,VARIANT_CLASS,SYMBOL_SOURCE,HGNC_ID,BIOTYPE,CANONICAL,MANE,CCDS,ENSP,SWISSPROT,TREMBL,UNIPARC,REFSEQ_MATCH,SOURCE,SIFT,PolyPhen,HGVS_OFFSET,AF,AFR_AF,AMR_AF,EAS_AF,EUR_AF,SAS_AF,AA_AF,EA_AF,gnomAD_AF,gnomAD_AFR_AF,gnomAD_AMR_AF,gnomAD_ASJ_AF,gnomAD_EAS_AF,gnomAD_FIN_AF,gnomAD_NFE_AF,gnomAD_OTH_AF,gnomAD_SAS_AF,SOMATIC,PHENO,OverlapBP,OverlapPC,1000Gp3_AC,1000Gp3_AF,1000Gp3_AFR_AC,1000Gp3_AFR_AF,1000Gp3_AMR_AC,1000Gp3_AMR_AF,1000Gp3_EAS_AC,1000Gp3_EAS_AF,1000Gp3_EUR_AC,1000Gp3_EUR_AF,1000Gp3_SAS_AC,1000Gp3_SAS_AF,ALSPAC_AC,ALSPAC_AF,AltaiNeandertal,Ancestral_allele,CADD_phred,CADD_raw,CADD_raw_rankscore,DANN_rankscore,DANN_score,Denisova,ESP6500_AA_AC,ESP6500_AA_AF,ESP6500_EA_AC,ESP6500_EA_AF,Eigen-PC-phred,Eigen-PC-raw,Eigen-PC-raw_rankscore,Eigen-phred,Eigen-raw,Eigen_coding_or_noncoding,ExAC_AFR_AC,ExAC_AFR_AF,ExAC_AMR_AC,ExAC_AMR_AF,ExAC_Adj_AC,ExAC_Adj_AF,ExAC_EAS_AC,ExAC_EAS_AF,ExAC_FIN_AC,ExAC_FIN_AF,ExAC_NFE_AC,ExAC_NFE_AF,ExAC_SAS_AC,ExAC_SAS_AF,ExAC_nonTCGA_AC,ExAC_nonTCGA_AF,ExAC_nonTCGA_AFR_AC,ExAC_nonTCGA_AFR_AF,ExAC_nonTCGA_AMR_AC,ExAC_nonTCGA_AMR_AF,ExAC_nonTCGA_Adj_AC,ExAC_nonTCGA_Adj_AF,ExAC_nonTCGA_EAS_AC,ExAC_nonTCGA_EAS_AF,ExAC_nonTCGA_FIN_AC,ExAC_nonTCGA_FIN_AF,ExAC_nonTCGA_NFE_AC,ExAC_nonTCGA_NFE_AF,ExAC_nonTCGA_SAS_AC,ExAC_nonTCGA_SAS_AF,ExAC_nonpsych_AC,ExAC_nonpsych_AF,ExAC_nonpsych_AFR_AC,ExAC_nonpsych_AFR_AF,ExAC_nonpsych_AMR_AC,ExAC_nonpsych_AMR_AF,ExAC_nonpsych_Adj_AC,ExAC_nonpsych_Adj_AF,ExAC_nonpsych_EAS_AC,ExAC_nonpsych_EAS_AF,ExAC_nonpsych_FIN_AC,ExAC_nonpsych_FIN_AF,ExAC_nonpsych_NFE_AC,ExAC_nonpsych_NFE_AF,ExAC_nonpsych_SAS_AC,ExAC_nonpsych_SAS_AF,FATHMM_converted_rankscore,FATHMM_pred,FATHMM_score,GERP++_NR,GERP++_RS,GERP++_RS_rankscore,GM12878_confidence_value,GM12878_fitCons_score,GM12878_fitCons_score_rankscore,GTEx_V6p_gene,GTEx_V6p_tissue,GenoCanyon_score,GenoCanyon_score_rankscore,H1-hESC_confidence_value,H1-hESC_fitCons_score,H1-hESC_fitCons_score_rankscore,clinvar_clnsig,clinvar_golden_stars,HUVEC_confidence_value,HUVEC_fitCons_score,HUVEC_fitCons_score_rankscore,LRT_Omega,LRT_converted_rankscore,LRT_pred,LRT_score,M-CAP_pred,M-CAP_rankscore,M-CAP_score,MetaLR_pred,MetaLR_rankscore,MetaLR_score,MetaSVM_pred,MetaSVM_rankscore,MetaSVM_score,MutPred_AAchange,MutPred_Top5features,MutPred_protID,MutPred_rankscore,MutPred_score,MutationAssessor_UniprotID,MutationAssessor_pred,MutationAssessor_score,MutationAssessor_score_rankscore,MutationAssessor_variant,MutationTaster_AAE,MutationTaster_converted_rankscore,MutationTaster_model,MutationTaster_pred,MutationTaster_score,PROVEAN_converted_rankscore,PROVEAN_pred,PROVEAN_score,Polyphen2_HDIV_pred,Polyphen2_HDIV_rankscore,Polyphen2_HDIV_score,Polyphen2_HVAR_pred,Polyphen2_HVAR_rankscore,Polyphen2_HVAR_score,REVEL_rankscore,REVEL_score,Reliability_index,SIFT_converted_rankscore,SIFT_pred,SIFT_score,SiPhy_29way_logOdds,SiPhy_29way_logOdds_rankscore,SiPhy_29way_pi,TWINSUK_AC,TWINSUK_AF,Transcript_id_VEST3,Transcript_var_VEST3,Uniprot_aapos_Polyphen2,Uniprot_acc_Polyphen2,Uniprot_id_Polyphen2,VEST3_rankscore,VEST3_score,aaalt,aapos,aaref,alt,cds_strand,chr,codon_degeneracy,codonpos,fathmm-MKL_coding_group,fathmm-MKL_coding_pred,fathmm-MKL_coding_rankscore,fathmm-MKL_coding_score,genename,gnomAD_exomes_AFR_AC,gnomAD_exomes_AFR_AF,gnomAD_exomes_AFR_AN,gnomAD_exomes_AMR_AC,gnomAD_exomes_AMR_AF,gnomAD_exomes_AMR_AN,gnomAD_exomes_AN,gnomAD_exomes_ASJ_AC,gnomAD_exomes_ASJ_AF,gnomAD_exomes_ASJ_AN,gnomAD_exomes_EAS_AC,gnomAD_exomes_EAS_AF,gnomAD_exomes_EAS_AN,gnomAD_exomes_FIN_AC,gnomAD_exomes_FIN_AF,gnomAD_exomes_FIN_AN,gnomAD_exomes_NFE_AC,gnomAD_exomes_NFE_AF,gnomAD_exomes_NFE_AN,gnomAD_exomes_OTH_AC,gnomAD_exomes_OTH_AF,gnomAD_exomes_OTH_AN,gnomAD_exomes_SAS_AC,gnomAD_exomes_SAS_AF,gnomAD_exomes_SAS_AN,gnomAD_genomes_AFR_AC,gnomAD_genomes_AFR_AF,gnomAD_genomes_AFR_AN,gnomAD_genomes_AMR_AC,gnomAD_genomes_AMR_AF,gnomAD_genomes_AMR_AN,gnomAD_genomes_AN,gnomAD_genomes_ASJ_AC,gnomAD_genomes_ASJ_AF,gnomAD_genomes_ASJ_AN,gnomAD_genomes_EAS_AC,gnomAD_genomes_EAS_AF,gnomAD_genomes_EAS_AN,gnomAD_genomes_FIN_AC,gnomAD_genomes_FIN_AF,gnomAD_genomes_FIN_AN,gnomAD_genomes_NFE_AC,gnomAD_genomes_NFE_AF,gnomAD_genomes_NFE_AN,gnomAD_genomes_OTH_AC,gnomAD_genomes_OTH_AF,gnomAD_genomes_OTH_AN,integrated_confidence_value,integrated_fitCons_score,integrated_fitCons_score_rankscore,phastCons100way_vertebrate,phastCons100way_vertebrate_rankscore,phastCons20way_mammalian,phastCons20way_mammalian_rankscore,phyloP100way_vertebrate,phyloP100way_vertebrate_rankscore,phyloP20way_mammalian,phyloP20way_mammalian_rankscore,pos(1-based),ref,refcodon,Condel' --custom /home/detagen/Desktop/programlar/ensembl-data/clinvar/clinvar_20190513.vcf.gz,ClinVar,vcf,exact,0,CLNSIG,CLNREVSTAT,CLNDN --plugin Phenotypes,file=/home/detagen/.vep/Plugin/Phenotypes.pm_homo_sapiens_97_GRCh37.gvf.gz,include_types=Gene

at7 commented 5 years ago

You should include PHENOTYPES into your fields list which you have already done. The problem you had last time was that there wasn't a description for the Mastermind column names but a ?. Do you mean that all rows of your output have a - in your PHENOTYPES column?

shigej38 commented 5 years ago

I have already added "PHENOTYPES" in --fields. However, when you add it in this way, all the rows in the column "PHENOTYPES" are (-). however, if I remove the --fields parameter, the column "PHENOTYPES" is filled with real information

at7 commented 5 years ago

Thank you for the clarification. However, I'm not able to reproduce the problem. If you use --fields the phenotype results will be in the second column. Without --fields phenotypes will show up towards the end of the columns. I cannot think of another reason why the annotation should be missing.

shigej38 commented 5 years ago

ı am trying again end result: my variables: `DIR=/home/$USER/Desktop/programlar

PLAYGROUND=/home/$USER/Desktop/pipeline/playground

RESULT=/home/$USER/Desktop/pipeline

LOG=$RESULT/log

G2PLOG=$LOG/g2plog

VEP=$DIR/ensembl-vep

VEPDATA=$DIR/ensembl-data

CACHE=/home/$USER/.vep

PHENO=$CACHE/Plugin/Phenotypes.pm_homo_sapiens_97_GRCh37.gvf.gz

SIRA="Uploaded_variation,PHENOTYPES,cDNA_position,REF_ALLELE,Allele,Protein_position,Amino_acids,Codons,SYMBOL,EXON,INTRON,ZYG,Consequence,CLIN_SIG,Existing_variation,rs_dbSNP150,G2P_complete,G2P_flag,G2P_gene_req,Mastermind_MMID3,Mastermind_counts,clinvar_rs,clinvar_trait,DOMAINS,Interpro_domain,hg18_chr,hg18_pos(1-based),hg19_chr,hg19_pos(1-based),ExAC_AC,ExAC_AF,gnomAD_exomes_AC,gnomAD_exomes_AF,gnomAD_genomes_AC,gnomAD_genomes_AF,Ensembl_geneid,Ensembl_proteinid,Ensembl_transcriptid,HGVSc,HGVSp,Location,Gene,Feature,Feature_type,CDS_position,IND,ALLELE_NUM,IMPACT,DISTANCE,STRAND,FLAGS,VARIANT_CLASS,SYMBOL_SOURCE,HGNC_ID,BIOTYPE,CANONICAL,MANE,CCDS,ENSP,SWISSPROT,TREMBL,UNIPARC,REFSEQ_MATCH,SOURCE,SIFT,PolyPhen,HGVS_OFFSET,AF,AFR_AF,AMR_AF,EAS_AF,EUR_AF,SAS_AF,AA_AF,EA_AF,gnomAD_AF,gnomAD_AFR_AF,gnomAD_AMR_AF,gnomAD_ASJ_AF,gnomAD_EAS_AF,gnomAD_FIN_AF,gnomAD_NFE_AF,gnomAD_OTH_AF,gnomAD_SAS_AF,SOMATIC,PHENO,OverlapBP,OverlapPC,1000Gp3_AC,1000Gp3_AF,1000Gp3_AFR_AC,1000Gp3_AFR_AF,1000Gp3_AMR_AC,1000Gp3_AMR_AF,1000Gp3_EAS_AC,1000Gp3_EAS_AF,1000Gp3_EUR_AC,1000Gp3_EUR_AF,1000Gp3_SAS_AC,1000Gp3_SAS_AF,ALSPAC_AC,ALSPAC_AF,AltaiNeandertal,Ancestral_allele,CADD_phred,CADD_raw,CADD_raw_rankscore,DANN_rankscore,DANN_score,Denisova,ESP6500_AA_AC,ESP6500_AA_AF,ESP6500_EA_AC,ESP6500_EA_AF,Eigen-PC-phred,Eigen-PC-raw,Eigen-PC-raw_rankscore,Eigen-phred,Eigen-raw,Eigen_coding_or_noncoding,ExAC_AFR_AC,ExAC_AFR_AF,ExAC_AMR_AC,ExAC_AMR_AF,ExAC_Adj_AC,ExAC_Adj_AF,ExAC_EAS_AC,ExAC_EAS_AF,ExAC_FIN_AC,ExAC_FIN_AF,ExAC_NFE_AC,ExAC_NFE_AF,ExAC_SAS_AC,ExAC_SAS_AF,ExAC_nonTCGA_AC,ExAC_nonTCGA_AF,ExAC_nonTCGA_AFR_AC,ExAC_nonTCGA_AFR_AF,ExAC_nonTCGA_AMR_AC,ExAC_nonTCGA_AMR_AF,ExAC_nonTCGA_Adj_AC,ExAC_nonTCGA_Adj_AF,ExAC_nonTCGA_EAS_AC,ExAC_nonTCGA_EAS_AF,ExAC_nonTCGA_FIN_AC,ExAC_nonTCGA_FIN_AF,ExAC_nonTCGA_NFE_AC,ExAC_nonTCGA_NFE_AF,ExAC_nonTCGA_SAS_AC,ExAC_nonTCGA_SAS_AF,ExAC_nonpsych_AC,ExAC_nonpsych_AF,ExAC_nonpsych_AFR_AC,ExAC_nonpsych_AFR_AF,ExAC_nonpsych_AMR_AC,ExAC_nonpsych_AMR_AF,ExAC_nonpsych_Adj_AC,ExAC_nonpsych_Adj_AF,ExAC_nonpsych_EAS_AC,ExAC_nonpsych_EAS_AF,ExAC_nonpsych_FIN_AC,ExAC_nonpsych_FIN_AF,ExAC_nonpsych_NFE_AC,ExAC_nonpsych_NFE_AF,ExAC_nonpsych_SAS_AC,ExAC_nonpsych_SAS_AF,FATHMM_converted_rankscore,FATHMM_pred,FATHMM_score,GERP++_NR,GERP++_RS,GERP++_RS_rankscore,GM12878_confidence_value,GM12878_fitCons_score,GM12878_fitCons_score_rankscore,GTEx_V6p_gene,GTEx_V6p_tissue,GenoCanyon_score,GenoCanyon_score_rankscore,H1-hESC_confidence_value,H1-hESC_fitCons_score,H1-hESC_fitCons_score_rankscore,clinvar_clnsig,clinvar_golden_stars,HUVEC_confidence_value,HUVEC_fitCons_score,HUVEC_fitCons_score_rankscore,LRT_Omega,LRT_converted_rankscore,LRT_pred,LRT_score,M-CAP_pred,M-CAP_rankscore,M-CAP_score,MetaLR_pred,MetaLR_rankscore,MetaLR_score,MetaSVM_pred,MetaSVM_rankscore,MetaSVM_score,MutPred_AAchange,MutPred_Top5features,MutPred_protID,MutPred_rankscore,MutPred_score,MutationAssessor_UniprotID,MutationAssessor_pred,MutationAssessor_score,MutationAssessor_score_rankscore,MutationAssessor_variant,MutationTaster_AAE,MutationTaster_converted_rankscore,MutationTaster_model,MutationTaster_pred,MutationTaster_score,PROVEAN_converted_rankscore,PROVEAN_pred,PROVEAN_score,Polyphen2_HDIV_pred,Polyphen2_HDIV_rankscore,Polyphen2_HDIV_score,Polyphen2_HVAR_pred,Polyphen2_HVAR_rankscore,Polyphen2_HVAR_score,REVEL_rankscore,REVEL_score,Reliability_index,SIFT_converted_rankscore,SIFT_pred,SIFT_score,SiPhy_29way_logOdds,SiPhy_29way_logOdds_rankscore,SiPhy_29way_pi,TWINSUK_AC,TWINSUK_AF,Transcript_id_VEST3,Transcript_var_VEST3,Uniprot_aapos_Polyphen2,Uniprot_acc_Polyphen2,Uniprot_id_Polyphen2,VEST3_rankscore,VEST3_score,aaalt,aapos,aaref,alt,cds_strand,chr,codon_degeneracy,codonpos,fathmm-MKL_coding_group,fathmm-MKL_coding_pred,fathmm-MKL_coding_rankscore,fathmm-MKL_coding_score,genename,gnomAD_exomes_AFR_AC,gnomAD_exomes_AFR_AF,gnomAD_exomes_AFR_AN,gnomAD_exomes_AMR_AC,gnomAD_exomes_AMR_AF,gnomAD_exomes_AMR_AN,gnomAD_exomes_AN,gnomAD_exomes_ASJ_AC,gnomAD_exomes_ASJ_AF,gnomAD_exomes_ASJ_AN,gnomAD_exomes_EAS_AC,gnomAD_exomes_EAS_AF,gnomAD_exomes_EAS_AN,gnomAD_exomes_FIN_AC,gnomAD_exomes_FIN_AF,gnomAD_exomes_FIN_AN,gnomAD_exomes_NFE_AC,gnomAD_exomes_NFE_AF,gnomAD_exomes_NFE_AN,gnomAD_exomes_OTH_AC,gnomAD_exomes_OTH_AF,gnomAD_exomes_OTH_AN,gnomAD_exomes_SAS_AC,gnomAD_exomes_SAS_AF,gnomAD_exomes_SAS_AN,gnomAD_genomes_AFR_AC,gnomAD_genomes_AFR_AF,gnomAD_genomes_AFR_AN,gnomAD_genomes_AMR_AC,gnomAD_genomes_AMR_AF,gnomAD_genomes_AMR_AN,gnomAD_genomes_AN,gnomAD_genomes_ASJ_AC,gnomAD_genomes_ASJ_AF,gnomAD_genomes_ASJ_AN,gnomAD_genomes_EAS_AC,gnomAD_genomes_EAS_AF,gnomAD_genomes_EAS_AN,gnomAD_genomes_FIN_AC,gnomAD_genomes_FIN_AF,gnomAD_genomes_FIN_AN,gnomAD_genomes_NFE_AC,gnomAD_genomes_NFE_AF,gnomAD_genomes_NFE_AN,gnomAD_genomes_OTH_AC,gnomAD_genomes_OTH_AF,gnomAD_genomes_OTH_AN,integrated_confidence_value,integrated_fitCons_score,integrated_fitCons_score_rankscore,phastCons100way_vertebrate,phastCons100way_vertebrate_rankscore,phastCons20way_mammalian,phastCons20way_mammalian_rankscore,phyloP100way_vertebrate,phyloP100way_vertebrate_rankscore,phyloP20way_mammalian,phyloP20way_mammalian_rankscore,pos(1-based),ref,refcodon,Condel"`

my used command is:

$VEP/vep --fork 1 --refseq --use_given_ref --force_overwrite --coding_only -i /home/detagen/Desktop/pipeline/playground/NECESSARY/FMF-248/FMF-248.vcf -o /home/detagen/Desktop/deneme.csv --cache --offline --assembly GRCh37 --tab --check_existing --biotype --canonical --domains --uniprot --ccds --symbol --protein --hgvs --no_escape --numbers --show_ref_allele --allele_number --individual all --regulatory --humdiv --polyphen p --sift p --variant_class --plugin dbNSFP,$VEPDATA/dbNSFP3.5/dbNSFP3.5.gz,ALL --plugin Condel,$CACHE/Plugins/config/Condel/config/condel_SP.conf,p --fasta $VEPDATA/fasta/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa --plugin Mastermind,$VEPDATA/mastermind/mastermind_cited_variants_reference-2019.06.14-grch37.vcf.gz --plugin G2P,file="$VEPDATA/G2P/DDG2P_10_7_2019.csv",log_dir="$LOGDIR/$FILE",txt_report="$LOGDIR/$FILE/$BASE.txt",html_report="$LOGDIR/$FILE/$BASE.html" --fields $SIRA --custom $VEPDATA/clinvar/clinvar_20190513.vcf.gz,ClinVar,vcf,exact,0,CLNSIG,CLNREVSTAT,CLNDN --plugin Phenotypes,file=$PHENO,include_types=Gene

my output file is: (note that the phenotype column is row (-)) `

Uploaded_variation PHENOTYPES cDNA_position REF_ALLELE Allele Protein_position Amino_acids Codons SYMBOL EXON INTRON ZYG Consequence CLIN_SIG Existing_variation rs_dbSNP150 G2P_complete G2P_flag G2P_gene_req Mastermind_MMID3 Mastermind_counts clinvar_rs clinvar_trait DOMAINS Interpro_domain hg18_chr hg18_pos(1-based) hg19_chr hg19_pos(1-based) ExAC_AC ExAC_AF gnomAD_exomes_AC gnomAD_exomes_AF gnomAD_genomes_AC gnomAD_genomes_AF Ensembl_geneid Ensembl_proteinid Ensembl_transcriptid HGVSc HGVSp Location Gene Feature Feature_type CDS_position IND ALLELE_NUM IMPACT DISTANCE STRAND FLAGS VARIANT_CLASS SYMBOL_SOURCE HGNC_ID BIOTYPE CANONICAL MANE CCDS ENSP SWISSPROT TREMBL UNIPARC REFSEQ_MATCH SOURCE SIFT PolyPhen HGVS_OFFSET AF AFR_AF AMR_AF EAS_AF EUR_AF SAS_AF AA_AF EA_AF gnomAD_AF gnomAD_AFR_AF gnomAD_AMR_AF gnomAD_ASJ_AF gnomAD_EAS_AF gnomAD_FIN_AF gnomAD_NFE_AF gnomAD_OTH_AF gnomAD_SAS_AF SOMATIC PHENO OverlapBP OverlapPC 1000Gp3_AC 1000Gp3_AF 1000Gp3_AFR_AC 1000Gp3_AFR_AF 1000Gp3_AMR_AC 1000Gp3_AMR_AF 1000Gp3_EAS_AC 1000Gp3_EAS_AF 1000Gp3_EUR_AC 1000Gp3_EUR_AF 1000Gp3_SAS_AC 1000Gp3_SAS_AF ALSPAC_AC ALSPAC_AF AltaiNeandertal Ancestral_allele CADD_phred CADD_raw CADD_raw_rankscore DANN_rankscore DANN_score Denisova ESP6500_AA_AC ESP6500_AA_AF ESP6500_EA_AC ESP6500_EA_AF Eigen-PC-phred Eigen-PC-raw Eigen-PC-raw_rankscore Eigen-phred Eigen-raw Eigen_coding_or_noncoding ExAC_AFR_AC ExAC_AFR_AF ExAC_AMR_AC ExAC_AMR_AF ExAC_Adj_AC ExAC_Adj_AF ExAC_EAS_AC ExAC_EAS_AF ExAC_FIN_AC ExAC_FIN_AF ExAC_NFE_AC ExAC_NFE_AF ExAC_SAS_AC ExAC_SAS_AF ExAC_nonTCGA_AC ExAC_nonTCGA_AF ExAC_nonTCGA_AFR_AC ExAC_nonTCGA_AFR_AF ExAC_nonTCGA_AMR_AC ExAC_nonTCGA_AMR_AF ExAC_nonTCGA_Adj_AC ExAC_nonTCGA_Adj_AF ExAC_nonTCGA_EAS_AC ExAC_nonTCGA_EAS_AF ExAC_nonTCGA_FIN_AC ExAC_nonTCGA_FIN_AF ExAC_nonTCGA_NFE_AC ExAC_nonTCGA_NFE_AF ExAC_nonTCGA_SAS_AC ExAC_nonTCGA_SAS_AF ExAC_nonpsych_AC ExAC_nonpsych_AF ExAC_nonpsych_AFR_AC ExAC_nonpsych_AFR_AF ExAC_nonpsych_AMR_AC ExAC_nonpsych_AMR_AF ExAC_nonpsych_Adj_AC ExAC_nonpsych_Adj_AF ExAC_nonpsych_EAS_AC ExAC_nonpsych_EAS_AF ExAC_nonpsych_FIN_AC ExAC_nonpsych_FIN_AF ExAC_nonpsych_NFE_AC ExAC_nonpsych_NFE_AF ExAC_nonpsych_SAS_AC ExAC_nonpsych_SAS_AF FATHMM_converted_rankscore FATHMM_pred FATHMM_score GERP++_NR GERP++_RS GERP++_RS_rankscore GM12878_confidence_value GM12878_fitCons_score GM12878_fitCons_score_rankscore GTEx_V6p_gene GTEx_V6p_tissue GenoCanyon_score GenoCanyon_score_rankscore H1-hESC_confidence_value H1-hESC_fitCons_score H1-hESC_fitCons_score_rankscore clinvar_clnsig clinvar_golden_stars HUVEC_confidence_value HUVEC_fitCons_score HUVEC_fitCons_score_rankscore LRT_Omega LRT_converted_rankscore LRT_pred LRT_score M-CAP_pred M-CAP_rankscore M-CAP_score MetaLR_pred MetaLR_rankscore MetaLR_score MetaSVM_pred MetaSVM_rankscore MetaSVM_score MutPred_AAchange MutPred_Top5features MutPred_protID MutPred_rankscore MutPred_score MutationAssessor_UniprotID MutationAssessor_pred MutationAssessor_score MutationAssessor_score_rankscore MutationAssessor_variant MutationTaster_AAE MutationTaster_converted_rankscore MutationTaster_model MutationTaster_pred MutationTaster_score PROVEAN_converted_rankscore PROVEAN_pred PROVEAN_score Polyphen2_HDIV_pred Polyphen2_HDIV_rankscore Polyphen2_HDIV_score Polyphen2_HVAR_pred Polyphen2_HVAR_rankscore Polyphen2_HVAR_score REVEL_rankscore REVEL_score Reliability_index SIFT_converted_rankscore SIFT_pred SIFT_score SiPhy_29way_logOdds SiPhy_29way_logOdds_rankscore SiPhy_29way_pi TWINSUK_AC TWINSUK_AF Transcript_id_VEST3 Transcript_var_VEST3 Uniprot_aapos_Polyphen2 Uniprot_acc_Polyphen2 Uniprot_id_Polyphen2 VEST3_rankscore VEST3_score aaalt aapos aaref alt cds_strand chr codon_degeneracy codonpos fathmm-MKL_coding_group fathmm-MKL_coding_pred fathmm-MKL_coding_rankscore fathmm-MKL_coding_score genename gnomAD_exomes_AFR_AC gnomAD_exomes_AFR_AF gnomAD_exomes_AFR_AN gnomAD_exomes_AMR_AC gnomAD_exomes_AMR_AF gnomAD_exomes_AMR_AN gnomAD_exomes_AN gnomAD_exomes_ASJ_AC gnomAD_exomes_ASJ_AF gnomAD_exomes_ASJ_AN gnomAD_exomes_EAS_AC gnomAD_exomes_EAS_AF gnomAD_exomes_EAS_AN gnomAD_exomes_FIN_AC gnomAD_exomes_FIN_AF gnomAD_exomes_FIN_AN gnomAD_exomes_NFE_AC gnomAD_exomes_NFE_AF gnomAD_exomes_NFE_AN gnomAD_exomes_OTH_AC gnomAD_exomes_OTH_AF gnomAD_exomes_OTH_AN gnomAD_exomes_SAS_AC gnomAD_exomes_SAS_AF gnomAD_exomes_SAS_AN gnomAD_genomes_AFR_AC gnomAD_genomes_AFR_AF gnomAD_genomes_AFR_AN gnomAD_genomes_AMR_AC gnomAD_genomes_AMR_AF gnomAD_genomes_AMR_AN gnomAD_genomes_AN gnomAD_genomes_ASJ_AC gnomAD_genomes_ASJ_AF gnomAD_genomes_ASJ_AN gnomAD_genomes_EAS_AC gnomAD_genomes_EAS_AF gnomAD_genomes_EAS_AN gnomAD_genomes_FIN_AC gnomAD_genomes_FIN_AF gnomAD_genomes_FIN_AN gnomAD_genomes_NFE_AC gnomAD_genomes_NFE_AF gnomAD_genomes_NFE_AN gnomAD_genomes_OTH_AC gnomAD_genomes_OTH_AF gnomAD_genomes_OTH_AN integrated_confidence_value integrated_fitCons_score integrated_fitCons_score_rankscore phastCons100way_vertebrate phastCons100way_vertebrate_rankscore phastCons20way_mammalian phastCons20way_mammalian_rankscore phyloP100way_vertebrate phyloP100way_vertebrate_rankscore phyloP20way_mammalian phyloP20way_mammalian_rankscore pos(1-based) ref refcodon Condel

chr1_11854457_G/A - 1591 G A 476 F ttC/ttT MTHFR 8/12 - HOM synonymous_variant benign rs4846051,CM044675 - - - - - - - - - - - - - - - - - - - - - - - NM_001330358.1:c.1428C>T NP_001317287.1:p.Phe476= chr1:11854457 4524 NM_001330358.1 Transcript 1428 FMF-248 1 LOW - -1 - SNV EntrezGene - protein_coding YES - - NP_001317287.1 - - - rseq_mrna_match - - - - 0.903 0.6558 0.9683 0.996 0.997 0.998 0.6827 0.997 0.9748 0.678 0.9819 0.9852 0.9991 1 0.9983 0.9839 0.9993 - 1,1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chr1_11854457_G/A - 1534 G A 435 F ttC/ttT MTHFR 8/12 - HOM synonymous_variant benign rs4846051,CM044675 - - - - MTHFR:F435F 3|6|19 - - - - - - - - - - - - - - - - - NM_005957.4:c.1305C>T NP_005948.3:p.Phe435= chr1:11854457 4524 NM_005957.4 Transcript 1305 FMF-248 1 LOW - -1 - SNV EntrezGene - protein_coding - - - NP_005948.3 - - - - - - - - 0.903 0.6558 0.9683 0.996 0.997 0.998 0.6827 0.997 0.9748 0.678 0.9819 0.9852 0.9991 1 0.9983 0.9839 0.9993 - 1,1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chr1_11854457_G/A - 2371 G A 476 F ttC/ttT MTHFR 8/12 - HOM synonymous_variant benign rs4846051,CM044675 - - - - - - - - - - - - - - - - - - - - - - - XM_005263458.1:c.1428C>T XP_005263515.1:p.Phe476= chr1:11854457 4524 XM_005263458.1 Transcript 1428 FMF-248 1 LOW - -1 - SNV EntrezGene - protein_coding YES - - XP_005263515.1 - - - - - - - - 0.903 0.6558 0.9683 0.996 0.997 0.998 0.6827 0.997 0.9748 0.678 0.9819 0.9852 0.9991 1 0.9983 0.9839 0.9993 - 1,1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chr1_11854457_G/A - 2646 G A 458 F ttC/ttT MTHFR 7/11 - HOM synonymous_variant benign rs4846051,CM044675 - - - - - - - - - - - - - - - - - - - - - - - XM_005263459.1:c.1374C>T XP_005263516.1:p.Phe458= chr1:11854457 4524 XM_005263459.1 Transcript 1374 FMF-248 1 LOW - -1 - SNV EntrezGene - protein_coding - - - XP_005263516.1 - - - - - - - - 0.903 0.6558 0.9683 0.996 0.997 0.998 0.6827 0.997 0.9748 0.678 0.9819 0.9852 0.9991 1 0.9983 0.9839 0.9993 - 1,1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chr1_11854457_G/A - 1973 G A 435 F ttC/ttT MTHFR 8/12 - HOM synonymous_variant benign rs4846051,CM044675 - - - - MTHFR:F435F 3|6|19 - - - - - - - - - - - - - - - - - XM_005263460.1:c.1305C>T XP_005263517.1:p.Phe435= chr1:11854457 4524 XM_005263460.1 Transcript 1305 FMF-248 1 LOW - -1 - SNV EntrezGene - protein_coding - - - XP_005263517.1 - - - - - - - - 0.903 0.6558 0.9683 0.996 0.997 0.998 0.6827 0.997 0.9748 0.678 0.9819 0.9852 0.9991 1 0.9983 0.9839 0.9993 - 1,1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chr1_11854457_G/A - 1869 G A 435 F ttC/ttT MTHFR 8/12 - HOM synonymous_variant benign rs4846051,CM044675 - - - - MTHFR:F435F 3|6|19 - - - - - - - - - - - - - - - - - XM_005263461.1:c.1305C>T XP_005263518.1:p.Phe435= chr1:11854457 4524 XM_005263461.1 Transcript 1305 FMF-248 1 LOW - -1 - SNV EntrezGene - protein_coding - - - XP_005263518.1 - - - - - - - - 0.903 0.6558 0.9683 0.996 0.997 0.998 0.6827 0.997 0.9748 0.678 0.9819 0.9852 0.9991 1 0.9983 0.9839 0.9993 - 1,1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chr1_11854457_G/A - 1336 G A 435 F ttC/ttT MTHFR 8/12 - HOM synonymous_variant benign rs4846051,CM044675 - - - - MTHFR:F435F 3|6|19 - - - - - - - - - - - - - - - - - XM_005263462.1:c.1305C>T XP_005263519.1:p.Phe435= chr1:11854457 4524 XM_005263462.1 Transcript 1305 FMF-248 1 LOW - -1 - SNV EntrezGene - protein_coding - - - XP_005263519.1 - - - - - - - - 0.903 0.6558 0.9683 0.996 0.997 0.998 0.6827 0.997 0.9748 0.678 0.9819 0.9852 0.9991 1 0.9983 0.9839 0.9993 - 1,1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chr1_11854457_G/A - 1551 G A 353 F ttC/ttT MTHFR 8/12 - HOM synonymous_variant benign rs4846051,CM044675 - - - - - - - - - - - - - - - - - - - - - - - XM_005263463.1:c.1059C>T XP_005263520.1:p.Phe353= chr1:11854457 4524 XM_005263463.1 Transcript 1059 FMF-248 1 LOW - -1 - SNV EntrezGene - protein_coding - - - XP_005263520.1 - - - - - - - - 0.903 0.6558 0.9683 0.996 0.997 0.998 0.6827 0.997 0.9748 0.678 0.9819 0.9852 0.9991 1 0.9983 0.9839 0.9993 - 1,1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chr1_11854476_T/G - 1572 T G 470 E/A gAa/gCa MTHFR 8/12 - HET missense_variant uncertain_significance,benign,likely_benign,other,risk_factor rs1801131,CM981315 rs1801131 - - - MTHFR:E470A,MTHFR:E429A 61|275|1230 rs1801131 MTHFR deficiency, thermolabile type&fluorouracil, leucovorin, and oxaliplatin response - Efficacy&Neural tube defects, folate-sensitive&not specified - - 1 11777063 1 11854476 35807 2.949e-01 71458 2.901848e-01 7990 2.589616e-01 ENSG00000177000 ENSP00000365777,ENSP00000365767,ENSP00000365775,ENSP00000365770 ENST00000376592,ENST00000376583,ENST00000376590,ENST00000376585 NM_001330358.1:c.1409A>C NP_001317287.1:p.Glu470Ala chr1:11854476 4524 NM_001330358.1 Transcript 1409 FMF-248 1 MODERATE - -1 - SNV EntrezGene - protein_coding YES - - NP_001317287.1 - - - rseq_mrna_match - tolerated(0.15) possibly_damaging(0.462) - 0.2494 0.1513 0.1513 0.2192 0.3131 0.4172 0.155 0.3131 0.289 0.1582 0.1594 0.2941 0.2198 0.3194 0.3186 0.2963 0.4116 - 1,1 - - 1249 0.2494009584664537 200 0.15128593040847202 105 0.15129682997118155 221 0.21924603174603174 315 0.31312127236580517 408 0.4171779141104294 1207 0.3131811105345096 ./. T 19.89 2.566020 0.36960 0.43665 0.98646129547053563 ./. 683 0.15501588742623695 2693 0.3131395348837209 2.162203 -0.0608863915964679 0.37161 2.001115 -0.156808186744175 c 1651 1.588e-01 1800 1.555e-01 35805 2.950e-01 1857 2.148e-01 2069 3.128e-01 21297 3.191e-01 6855 4.153e-01 31308 2.948e-01 1429 1.578e-01 1733 1.546e-01 31308 2.949e-01 1685 2.145e-01 2069 3.128e-01 17354 3.193e-01 6818 4.157e-01 25932 2.857e-01 1648 1.588e-01 1795 1.552e-01 25930 2.858e-01 1170 2.075e-01 1200 3.156e-01 13045 3.096e-01 6851 4.153e-01 0.73639 T,T,T,T -0.78,-0.78,-0.78,-0.78 4.74 4.74 0.59564 0 0.702456 0.74369 ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000011021.17&ENSG00000177000.6&ENSG00000177000.6&ENSG00000242349.1&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000011021.17&ENSG00000242349.1&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000011021.17&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000011021.17&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6 Adipose_Subcutaneous&Adipose_Visceral_Omentum&Artery_Aorta&Artery_Tibial&Artery_Tibial&Brain_Caudate_basal_ganglia&Brain_Cerebellum&Brain_Cerebellum&Brain_Cortex&Brain_Nucleus_accumbens_basal_ganglia&Breast_Mammary_Tissue&Cells_Transformed_fibroblasts&Cells_Transformed_fibroblasts&Cells_Transformed_fibroblasts&Colon_Sigmoid&Colon_Transverse&Esophagus_Mucosa&Esophagus_Muscularis&Esophagus_Muscularis&Lung&Muscle_Skeletal&Nerve_Tibial&Pancreas&Skin_Not_Sun_Exposed_Suprapubic&Skin_Not_Sun_Exposed_Suprapubic&Skin_Sun_Exposed_Lower_leg&Thyroid&Whole_Blood 0.99999999932141 0.74713 0 0.743671 0.96052 2&6&3&2 0&3&1&1 0 0.714379 0.83238 0.095160 0.62918 D 0.000001 - - - T 0.00011 0.0000 T 0.08152 -1.0759 - - - - - MTHR_HUMAN L 1.45 0.36831 E429A E470A,E470A,E429A,E429A 0.58814 simple_aae,simple_aae,simple_aae,simple_aae P,P,P,P 1.65022e-06,1.65022e-06,1.65022e-06,1.65022e-06 0.63397 D -3.09 B,P 0.34532 0.021,0.462 B 0.25850 0.009,0.065 0.48422 0.197 9 0.30473 T 0.1,0.135,0.1,0.135 13.7416 0.62174 0.0:0.0:0.0:1.0 1205 0.3249730312837109 ENST00000376583,ENST00000376585,ENST00000376592,NM_005957.4,ENST00000376590 E470A,E470A,E429A,E429A,E429A 429,470 P42898,Q5SNW6 MTHR_HUMAN,. 0.45614 0.391,0.387,0.391,0.391,0.397 A 429,470,429,470 E G - 1 0 2 AEFDBCI D 0.67133 0.96060 MTHFR 2417 1.579326e-01 15304 5373 1.600060e-01 33580 246250 2906 2.950254e-01 9850 3780 2.191813e-01 17246 7139 3.201632e-01 22298 35620 3.188728e-01 111706 1565 2.853756e-01 5484 12658 4.112143e-01 30782 1445 1.663214e-01 8688 154 1.837709e-01 838 30854 87 2.880795e-01 302 364 2.255266e-01 1614 1079 3.089920e-01 3492 4593 3.074297e-01 14940 268 2.734694e-01 980 0 0.732398 0.92378 0.968000 0.33884 0.914000 0.39028 3.756000 0.54670 1.061000 0.80716 11794419 T GAA neutral chr1_11854476_T/G - 1515 T G 429 E/A gAa/gCa MTHFR 8/12 - HET missense_variant uncertain_significance,benign,likely_benign,other,risk_factor rs1801131,CM981315 rs1801131 - - - MTHFR:E470A,MTHFR:E429A 61|275|1230 rs1801131 MTHFR deficiency, thermolabile type&fluorouracil, leucovorin, and oxaliplatin response - Efficacy&Neural tube defects, folate-sensitive&not specified - - 1 11777063 1 11854476 35807 2.949e-01 71458 2.901848e-01 7990 2.589616e-01 ENSG00000177000 ENSP00000365777,ENSP00000365767,ENSP00000365775,ENSP00000365770 ENST00000376592,ENST00000376583,ENST00000376590,ENST00000376585 NM_005957.4:c.1286A>C NP_005948.3:p.Glu429Ala chr1:11854476 4524 NM_005957.4 Transcript 1286 FMF-248 1 MODERATE - -1 - SNV EntrezGene - protein_coding - - - NP_005948.3 - - - - - tolerated(0.14) benign(0.021) - 0.2494 0.1513 0.1513 0.2192 0.3131 0.4172 0.155 0.3131 0.289 0.1582 0.1594 0.2941 0.2198 0.3194 0.3186 0.2963 0.4116 - 1,1 - - 1249 0.2494009584664537 200 0.15128593040847202 105 0.15129682997118155 221 0.21924603174603174 315 0.31312127236580517 408 0.4171779141104294 1207 0.3131811105345096 ./. T 19.89 2.566020 0.36960 0.43665 0.98646129547053563 ./. 683 0.15501588742623695 2693 0.3131395348837209 2.162203 -0.0608863915964679 0.37161 2.001115 -0.156808186744175 c 1651 1.588e-01 1800 1.555e-01 35805 2.950e-01 1857 2.148e-01 2069 3.128e-01 21297 3.191e-01 6855 4.153e-01 31308 2.948e-01 1429 1.578e-01 1733 1.546e-01 31308 2.949e-01 1685 2.145e-01 2069 3.128e-01 17354 3.193e-01 6818 4.157e-01 25932 2.857e-01 1648 1.588e-01 1795 1.552e-01 25930 2.858e-01 1170 2.075e-01 1200 3.156e-01 13045 3.096e-01 6851 4.153e-01 0.73639 T,T,T,T -0.78,-0.78,-0.78,-0.78 4.74 4.74 0.59564 0 0.702456 0.74369 ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000011021.17&ENSG00000177000.6&ENSG00000177000.6&ENSG00000242349.1&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000011021.17&ENSG00000242349.1&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000011021.17&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000011021.17&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6 Adipose_Subcutaneous&Adipose_Visceral_Omentum&Artery_Aorta&Artery_Tibial&Artery_Tibial&Brain_Caudate_basal_ganglia&Brain_Cerebellum&Brain_Cerebellum&Brain_Cortex&Brain_Nucleus_accumbens_basal_ganglia&Breast_Mammary_Tissue&Cells_Transformed_fibroblasts&Cells_Transformed_fibroblasts&Cells_Transformed_fibroblasts&Colon_Sigmoid&Colon_Transverse&Esophagus_Mucosa&Esophagus_Muscularis&Esophagus_Muscularis&Lung&Muscle_Skeletal&Nerve_Tibial&Pancreas&Skin_Not_Sun_Exposed_Suprapubic&Skin_Not_Sun_Exposed_Suprapubic&Skin_Sun_Exposed_Lower_leg&Thyroid&Whole_Blood 0.99999999932141 0.74713 0 0.743671 0.96052 2&6&3&2 0&3&1&1 0 0.714379 0.83238 0.095160 0.62918 D 0.000001 - - - T 0.00011 0.0000 T 0.08152 -1.0759 - - - - - MTHR_HUMAN L 1.45 0.36831 E429A E470A,E470A,E429A,E429A 0.58814 simple_aae,simple_aae,simple_aae,simple_aae P,P,P,P 1.65022e-06,1.65022e-06,1.65022e-06,1.65022e-06 0.63397 D -3.09 B,P 0.34532 0.021,0.462 B 0.25850 0.009,0.065 0.48422 0.197 9 0.30473 T 0.1,0.135,0.1,0.135 13.7416 0.62174 0.0:0.0:0.0:1.0 1205 0.3249730312837109 ENST00000376583,ENST00000376585,ENST00000376592,NM_005957.4,ENST00000376590 E470A,E470A,E429A,E429A,E429A 429,470 P42898,Q5SNW6 MTHR_HUMAN,. 0.45614 0.391,0.387,0.391,0.391,0.397 A 429,470,429,470 E G - 1 0 2 AEFDBCI D 0.67133 0.96060 MTHFR 2417 1.579326e-01 15304 5373 1.600060e-01 33580 246250 2906 2.950254e-01 9850 3780 2.191813e-01 17246 7139 3.201632e-01 22298 35620 3.188728e-01 111706 1565 2.853756e-01 5484 12658 4.112143e-01 30782 1445 1.663214e-01 8688 154 1.837709e-01 838 30854 87 2.880795e-01 302 364 2.255266e-01 1614 1079 3.089920e-01 3492 4593 3.074297e-01 14940 268 2.734694e-01 980 0 0.732398 0.92378 0.968000 0.33884 0.914000 0.39028 3.756000 0.54670 1.061000 0.80716 11794419 T GAA neutral chr1_11854476_T/G - 2352 T G 470 E/A gAa/gCa MTHFR 8/12 - HET missense_variant uncertain_significance,benign,likely_benign,other,risk_factor rs1801131,CM981315 rs1801131 - - - MTHFR:E470A,MTHFR:E429A 61|275|1230 rs1801131 MTHFR deficiency, thermolabile type&fluorouracil, leucovorin, and oxaliplatin response - Efficacy&Neural tube defects, folate-sensitive&not specified - - 1 11777063 1 11854476 35807 2.949e-01 71458 2.901848e-01 7990 2.589616e-01 ENSG00000177000 ENSP00000365777,ENSP00000365767,ENSP00000365775,ENSP00000365770 ENST00000376592,ENST00000376583,ENST00000376590,ENST00000376585 XM_005263458.1:c.1409A>C XP_005263515.1:p.Glu470Ala chr1:11854476 4524 XM_005263458.1 Transcript 1409 FMF-248 1 MODERATE - -1 - SNV EntrezGene - protein_coding YES - - XP_005263515.1 - - - - - tolerated(0.15) possibly_damaging(0.462) - 0.2494 0.1513 0.1513 0.2192 0.3131 0.4172 0.155 0.3131 0.289 0.1582 0.1594 0.2941 0.2198 0.3194 0.3186 0.2963 0.4116 - 1,1 - - 1249 0.2494009584664537 200 0.15128593040847202 105 0.15129682997118155 221 0.21924603174603174 315 0.31312127236580517 408 0.4171779141104294 1207 0.3131811105345096 ./. T 19.89 2.566020 0.36960 0.43665 0.98646129547053563 ./. 683 0.15501588742623695 2693 0.3131395348837209 2.162203 -0.0608863915964679 0.37161 2.001115 -0.156808186744175 c 1651 1.588e-01 1800 1.555e-01 35805 2.950e-01 1857 2.148e-01 2069 3.128e-01 21297 3.191e-01 6855 4.153e-01 31308 2.948e-01 1429 1.578e-01 1733 1.546e-01 31308 2.949e-01 1685 2.145e-01 2069 3.128e-01 17354 3.193e-01 6818 4.157e-01 25932 2.857e-01 1648 1.588e-01 1795 1.552e-01 25930 2.858e-01 1170 2.075e-01 1200 3.156e-01 13045 3.096e-01 6851 4.153e-01 0.73639 T,T,T,T -0.78,-0.78,-0.78,-0.78 4.74 4.74 0.59564 0 0.702456 0.74369 ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000011021.17&ENSG00000177000.6&ENSG00000177000.6&ENSG00000242349.1&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000011021.17&ENSG00000242349.1&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000011021.17&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000011021.17&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6 Adipose_Subcutaneous&Adipose_Visceral_Omentum&Artery_Aorta&Artery_Tibial&Artery_Tibial&Brain_Caudate_basal_ganglia&Brain_Cerebellum&Brain_Cerebellum&Brain_Cortex&Brain_Nucleus_accumbens_basal_ganglia&Breast_Mammary_Tissue&Cells_Transformed_fibroblasts&Cells_Transformed_fibroblasts&Cells_Transformed_fibroblasts&Colon_Sigmoid&Colon_Transverse&Esophagus_Mucosa&Esophagus_Muscularis&Esophagus_Muscularis&Lung&Muscle_Skeletal&Nerve_Tibial&Pancreas&Skin_Not_Sun_Exposed_Suprapubic&Skin_Not_Sun_Exposed_Suprapubic&Skin_Sun_Exposed_Lower_leg&Thyroid&Whole_Blood 0.99999999932141 0.74713 0 0.743671 0.96052 2&6&3&2 0&3&1&1 0 0.714379 0.83238 0.095160 0.62918 D 0.000001 - - - T 0.00011 0.0000 T 0.08152 -1.0759 - - - - - MTHR_HUMAN L 1.45 0.36831 E429A E470A,E470A,E429A,E429A 0.58814 simple_aae,simple_aae,simple_aae,simple_aae P,P,P,P 1.65022e-06,1.65022e-06,1.65022e-06,1.65022e-06 0.63397 D -3.09 B,P 0.34532 0.021,0.462 B 0.25850 0.009,0.065 0.48422 0.197 9 0.30473 T 0.1,0.135,0.1,0.135 13.7416 0.62174 0.0:0.0:0.0:1.0 1205 0.3249730312837109 ENST00000376583,ENST00000376585,ENST00000376592,NM_005957.4,ENST00000376590 E470A,E470A,E429A,E429A,E429A 429,470 P42898,Q5SNW6 MTHR_HUMAN,. 0.45614 0.391,0.387,0.391,0.391,0.397 A 429,470,429,470 E G - 1 0 2 AEFDBCI D 0.67133 0.96060 MTHFR 2417 1.579326e-01 15304 5373 1.600060e-01 33580 246250 2906 2.950254e-01 9850 3780 2.191813e-01 17246 7139 3.201632e-01 22298 35620 3.188728e-01 111706 1565 2.853756e-01 5484 12658 4.112143e-01 30782 1445 1.663214e-01 8688 154 1.837709e-01 838 30854 87 2.880795e-01 302 364 2.255266e-01 1614 1079 3.089920e-01 3492 4593 3.074297e-01 14940 268 2.734694e-01 980 0 0.732398 0.92378 0.968000 0.33884 0.914000 0.39028 3.756000 0.54670 1.061000 0.80716 11794419 T GAA neutral chr1_11854476_T/G - 2627 T G 452 E/A gAa/gCa MTHFR 7/11 - HET missense_variant uncertain_significance,benign,likely_benign,other,risk_factor rs1801131,CM981315 rs1801131 - - - - - rs1801131 MTHFR deficiency, thermolabile type&fluorouracil, leucovorin, and oxaliplatin response - Efficacy&Neural tube defects, folate-sensitive&not specified - - 1 11777063 1 11854476 35807 2.949e-01 71458 2.901848e-01 7990 2.589616e-01 ENSG00000177000 ENSP00000365777,ENSP00000365767,ENSP00000365775,ENSP00000365770 ENST00000376592,ENST00000376583,ENST00000376590,ENST00000376585 XM_005263459.1:c.1355A>C XP_005263516.1:p.Glu452Ala chr1:11854476 4524 XM_005263459.1 Transcript 1355 FMF-248 1 MODERATE - -1 - SNV EntrezGene - protein_coding - - - XP_005263516.1 - - - - - - - - 0.2494 0.1513 0.1513 0.2192 0.3131 0.4172 0.155 0.3131 0.289 0.1582 0.1594 0.2941 0.2198 0.3194 0.3186 0.2963 0.4116 - 1,1 - - 1249 0.2494009584664537 200 0.15128593040847202 105 0.15129682997118155 221 0.21924603174603174 315 0.31312127236580517 408 0.4171779141104294 1207 0.3131811105345096 ./. T 19.89 2.566020 0.36960 0.43665 0.98646129547053563 ./. 683 0.15501588742623695 2693 0.3131395348837209 2.162203 -0.0608863915964679 0.37161 2.001115 -0.156808186744175 c 1651 1.588e-01 1800 1.555e-01 35805 2.950e-01 1857 2.148e-01 2069 3.128e-01 21297 3.191e-01 6855 4.153e-01 31308 2.948e-01 1429 1.578e-01 1733 1.546e-01 31308 2.949e-01 1685 2.145e-01 2069 3.128e-01 17354 3.193e-01 6818 4.157e-01 25932 2.857e-01 1648 1.588e-01 1795 1.552e-01 25930 2.858e-01 1170 2.075e-01 1200 3.156e-01 13045 3.096e-01 6851 4.153e-01 0.73639 T,T,T,T -0.78,-0.78,-0.78,-0.78 4.74 4.74 0.59564 0 0.702456 0.74369 ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000011021.17&ENSG00000177000.6&ENSG00000177000.6&ENSG00000242349.1&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000011021.17&ENSG00000242349.1&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000011021.17&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000011021.17&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6 Adipose_Subcutaneous&Adipose_Visceral_Omentum&Artery_Aorta&Artery_Tibial&Artery_Tibial&Brain_Caudate_basal_ganglia&Brain_Cerebellum&Brain_Cerebellum&Brain_Cortex&Brain_Nucleus_accumbens_basal_ganglia&Breast_Mammary_Tissue&Cells_Transformed_fibroblasts&Cells_Transformed_fibroblasts&Cells_Transformed_fibroblasts&Colon_Sigmoid&Colon_Transverse&Esophagus_Mucosa&Esophagus_Muscularis&Esophagus_Muscularis&Lung&Muscle_Skeletal&Nerve_Tibial&Pancreas&Skin_Not_Sun_Exposed_Suprapubic&Skin_Not_Sun_Exposed_Suprapubic&Skin_Sun_Exposed_Lower_leg&Thyroid&Whole_Blood 0.99999999932141 0.74713 0 0.743671 0.96052 2&6&3&2 0&3&1&1 0 0.714379 0.83238 0.095160 0.62918 D 0.000001 - - - T 0.00011 0.0000 T 0.08152 -1.0759 - - - - - MTHR_HUMAN L 1.45 0.36831 E429A E470A,E470A,E429A,E429A 0.58814 simple_aae,simple_aae,simple_aae,simple_aae P,P,P,P 1.65022e-06,1.65022e-06,1.65022e-06,1.65022e-06 0.63397 D -3.09 B,P 0.34532 0.021,0.462 B 0.25850 0.009,0.065 0.48422 0.197 9 0.30473 T 0.1,0.135,0.1,0.135 13.7416 0.62174 0.0:0.0:0.0:1.0 1205 0.3249730312837109 ENST00000376583,ENST00000376585,ENST00000376592,NM_005957.4,ENST00000376590 E470A,E470A,E429A,E429A,E429A 429,470 P42898,Q5SNW6 MTHR_HUMAN,. 0.45614 0.391,0.387,0.391,0.391,0.397 A 429,470,429,470 E G - 1 0 2 AEFDBCI D 0.67133 0.96060 MTHFR 2417 1.579326e-01 15304 5373 1.600060e-01 33580 246250 2906 2.950254e-01 9850 3780 2.191813e-01 17246 7139 3.201632e-01 22298 35620 3.188728e-01 111706 1565 2.853756e-01 5484 12658 4.112143e-01 30782 1445 1.663214e-01 8688 154 1.837709e-01 838 30854 87 2.880795e-01 302 364 2.255266e-01 1614 1079 3.089920e-01 3492 4593 3.074297e-01 14940 268 2.734694e-01 980 0 0.732398 0.92378 0.968000 0.33884 0.914000 0.39028 3.756000 0.54670 1.061000 0.80716 11794419 T GAA - chr1_11854476_T/G - 1954 T G 429 E/A gAa/gCa MTHFR 8/12 - HET missense_variant uncertain_significance,benign,likely_benign,other,risk_factor rs1801131,CM981315 rs1801131 - - - MTHFR:E470A,MTHFR:E429A 61|275|1230 rs1801131 MTHFR deficiency, thermolabile type&fluorouracil, leucovorin, and oxaliplatin response - Efficacy&Neural tube defects, folate-sensitive&not specified - - 1 11777063 1 11854476 35807 2.949e-01 71458 2.901848e-01 7990 2.589616e-01 ENSG00000177000 ENSP00000365777,ENSP00000365767,ENSP00000365775,ENSP00000365770 ENST00000376592,ENST00000376583,ENST00000376590,ENST00000376585 XM_005263460.1:c.1286A>C XP_005263517.1:p.Glu429Ala chr1:11854476 4524 XM_005263460.1 Transcript 1286 FMF-248 1 MODERATE - -1 - SNV EntrezGene - protein_coding - - - XP_005263517.1 - - - - - tolerated(0.14) benign(0.021) - 0.2494 0.1513 0.1513 0.2192 0.3131 0.4172 0.155 0.3131 0.289 0.1582 0.1594 0.2941 0.2198 0.3194 0.3186 0.2963 0.4116 - 1,1 - - 1249 0.2494009584664537 200 0.15128593040847202 105 0.15129682997118155 221 0.21924603174603174 315 0.31312127236580517 408 0.4171779141104294 1207 0.3131811105345096 ./. T 19.89 2.566020 0.36960 0.43665 0.98646129547053563 ./. 683 0.15501588742623695 2693 0.3131395348837209 2.162203 -0.0608863915964679 0.37161 2.001115 -0.156808186744175 c 1651 1.588e-01 1800 1.555e-01 35805 2.950e-01 1857 2.148e-01 2069 3.128e-01 21297 3.191e-01 6855 4.153e-01 31308 2.948e-01 1429 1.578e-01 1733 1.546e-01 31308 2.949e-01 1685 2.145e-01 2069 3.128e-01 17354 3.193e-01 6818 4.157e-01 25932 2.857e-01 1648 1.588e-01 1795 1.552e-01 25930 2.858e-01 1170 2.075e-01 1200 3.156e-01 13045 3.096e-01 6851 4.153e-01 0.73639 T,T,T,T -0.78,-0.78,-0.78,-0.78 4.74 4.74 0.59564 0 0.702456 0.74369 ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000011021.17&ENSG00000177000.6&ENSG00000177000.6&ENSG00000242349.1&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000011021.17&ENSG00000242349.1&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000011021.17&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000011021.17&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6 Adipose_Subcutaneous&Adipose_Visceral_Omentum&Artery_Aorta&Artery_Tibial&Artery_Tibial&Brain_Caudate_basal_ganglia&Brain_Cerebellum&Brain_Cerebellum&Brain_Cortex&Brain_Nucleus_accumbens_basal_ganglia&Breast_Mammary_Tissue&Cells_Transformed_fibroblasts&Cells_Transformed_fibroblasts&Cells_Transformed_fibroblasts&Colon_Sigmoid&Colon_Transverse&Esophagus_Mucosa&Esophagus_Muscularis&Esophagus_Muscularis&Lung&Muscle_Skeletal&Nerve_Tibial&Pancreas&Skin_Not_Sun_Exposed_Suprapubic&Skin_Not_Sun_Exposed_Suprapubic&Skin_Sun_Exposed_Lower_leg&Thyroid&Whole_Blood 0.99999999932141 0.74713 0 0.743671 0.96052 2&6&3&2 0&3&1&1 0 0.714379 0.83238 0.095160 0.62918 D 0.000001 - - - T 0.00011 0.0000 T 0.08152 -1.0759 - - - - - MTHR_HUMAN L 1.45 0.36831 E429A E470A,E470A,E429A,E429A 0.58814 simple_aae,simple_aae,simple_aae,simple_aae P,P,P,P 1.65022e-06,1.65022e-06,1.65022e-06,1.65022e-06 0.63397 D -3.09 B,P 0.34532 0.021,0.462 B 0.25850 0.009,0.065 0.48422 0.197 9 0.30473 T 0.1,0.135,0.1,0.135 13.7416 0.62174 0.0:0.0:0.0:1.0 1205 0.3249730312837109 ENST00000376583,ENST00000376585,ENST00000376592,NM_005957.4,ENST00000376590 E470A,E470A,E429A,E429A,E429A 429,470 P42898,Q5SNW6 MTHR_HUMAN,. 0.45614 0.391,0.387,0.391,0.391,0.397 A 429,470,429,470 E G - 1 0 2 AEFDBCI D 0.67133 0.96060 MTHFR 2417 1.579326e-01 15304 5373 1.600060e-01 33580 246250 2906 2.950254e-01 9850 3780 2.191813e-01 17246 7139 3.201632e-01 22298 35620 3.188728e-01 111706 1565 2.853756e-01 5484 12658 4.112143e-01 30782 1445 1.663214e-01 8688 154 1.837709e-01 838 30854 87 2.880795e-01 302 364 2.255266e-01 1614 1079 3.089920e-01 3492 4593 3.074297e-01 14940 268 2.734694e-01 980 0 0.732398 0.92378 0.968000 0.33884 0.914000 0.39028 3.756000 0.54670 1.061000 0.80716 11794419 T GAA neutral chr1_11854476_T/G - 1850 T G 429 E/A gAa/gCa MTHFR 8/12 - HET missense_variant uncertain_significance,benign,likely_benign,other,risk_factor rs1801131,CM981315 rs1801131 - - - MTHFR:E470A,MTHFR:E429A 61|275|1230 rs1801131 MTHFR deficiency, thermolabile type&fluorouracil, leucovorin, and oxaliplatin response - Efficacy&Neural tube defects, folate-sensitive&not specified - - 1 11777063 1 11854476 35807 2.949e-01 71458 2.901848e-01 7990 2.589616e-01 ENSG00000177000 ENSP00000365777,ENSP00000365767,ENSP00000365775,ENSP00000365770 ENST00000376592,ENST00000376583,ENST00000376590,ENST00000376585 XM_005263461.1:c.1286A>C XP_005263518.1:p.Glu429Ala chr1:11854476 4524 XM_005263461.1 Transcript 1286 FMF-248 1 MODERATE - -1 - SNV EntrezGene - protein_coding - - - XP_005263518.1 - - - - - tolerated(0.14) benign(0.021) - 0.2494 0.1513 0.1513 0.2192 0.3131 0.4172 0.155 0.3131 0.289 0.1582 0.1594 0.2941 0.2198 0.3194 0.3186 0.2963 0.4116 - 1,1 - - 1249 0.2494009584664537 200 0.15128593040847202 105 0.15129682997118155 221 0.21924603174603174 315 0.31312127236580517 408 0.4171779141104294 1207 0.3131811105345096 ./. T 19.89 2.566020 0.36960 0.43665 0.98646129547053563 ./. 683 0.15501588742623695 2693 0.3131395348837209 2.162203 -0.0608863915964679 0.37161 2.001115 -0.156808186744175 c 1651 1.588e-01 1800 1.555e-01 35805 2.950e-01 1857 2.148e-01 2069 3.128e-01 21297 3.191e-01 6855 4.153e-01 31308 2.948e-01 1429 1.578e-01 1733 1.546e-01 31308 2.949e-01 1685 2.145e-01 2069 3.128e-01 17354 3.193e-01 6818 4.157e-01 25932 2.857e-01 1648 1.588e-01 1795 1.552e-01 25930 2.858e-01 1170 2.075e-01 1200 3.156e-01 13045 3.096e-01 6851 4.153e-01 0.73639 T,T,T,T -0.78,-0.78,-0.78,-0.78 4.74 4.74 0.59564 0 0.702456 0.74369 ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000011021.17&ENSG00000177000.6&ENSG00000177000.6&ENSG00000242349.1&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000011021.17&ENSG00000242349.1&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000011021.17&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000011021.17&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6 Adipose_Subcutaneous&Adipose_Visceral_Omentum&Artery_Aorta&Artery_Tibial&Artery_Tibial&Brain_Caudate_basal_ganglia&Brain_Cerebellum&Brain_Cerebellum&Brain_Cortex&Brain_Nucleus_accumbens_basal_ganglia&Breast_Mammary_Tissue&Cells_Transformed_fibroblasts&Cells_Transformed_fibroblasts&Cells_Transformed_fibroblasts&Colon_Sigmoid&Colon_Transverse&Esophagus_Mucosa&Esophagus_Muscularis&Esophagus_Muscularis&Lung&Muscle_Skeletal&Nerve_Tibial&Pancreas&Skin_Not_Sun_Exposed_Suprapubic&Skin_Not_Sun_Exposed_Suprapubic&Skin_Sun_Exposed_Lower_leg&Thyroid&Whole_Blood 0.99999999932141 0.74713 0 0.743671 0.96052 2&6&3&2 0&3&1&1 0 0.714379 0.83238 0.095160 0.62918 D 0.000001 - - - T 0.00011 0.0000 T 0.08152 -1.0759 - - - - - MTHR_HUMAN L 1.45 0.36831 E429A E470A,E470A,E429A,E429A 0.58814 simple_aae,simple_aae,simple_aae,simple_aae P,P,P,P 1.65022e-06,1.65022e-06,1.65022e-06,1.65022e-06 0.63397 D -3.09 B,P 0.34532 0.021,0.462 B 0.25850 0.009,0.065 0.48422 0.197 9 0.30473 T 0.1,0.135,0.1,0.135 13.7416 0.62174 0.0:0.0:0.0:1.0 1205 0.3249730312837109 ENST00000376583,ENST00000376585,ENST00000376592,NM_005957.4,ENST00000376590 E470A,E470A,E429A,E429A,E429A 429,470 P42898,Q5SNW6 MTHR_HUMAN,. 0.45614 0.391,0.387,0.391,0.391,0.397 A 429,470,429,470 E G - 1 0 2 AEFDBCI D 0.67133 0.96060 MTHFR 2417 1.579326e-01 15304 5373 1.600060e-01 33580 246250 2906 2.950254e-01 9850 3780 2.191813e-01 17246 7139 3.201632e-01 22298 35620 3.188728e-01 111706 1565 2.853756e-01 5484 12658 4.112143e-01 30782 1445 1.663214e-01 8688 154 1.837709e-01 838 30854 87 2.880795e-01 302 364 2.255266e-01 1614 1079 3.089920e-01 3492 4593 3.074297e-01 14940 268 2.734694e-01 980 0 0.732398 0.92378 0.968000 0.33884 0.914000 0.39028 3.756000 0.54670 1.061000 0.80716 11794419 T GAA neutral chr1_11854476_T/G - 1317 T G 429 E/A gAa/gCa MTHFR 8/12 - HET missense_variant uncertain_significance,benign,likely_benign,other,risk_factor rs1801131,CM981315 rs1801131 - - - MTHFR:E470A,MTHFR:E429A 61|275|1230 rs1801131 MTHFR deficiency, thermolabile type&fluorouracil, leucovorin, and oxaliplatin response - Efficacy&Neural tube defects, folate-sensitive&not specified - - 1 11777063 1 11854476 35807 2.949e-01 71458 2.901848e-01 7990 2.589616e-01 ENSG00000177000 ENSP00000365777,ENSP00000365767,ENSP00000365775,ENSP00000365770 ENST00000376592,ENST00000376583,ENST00000376590,ENST00000376585 XM_005263462.1:c.1286A>C XP_005263519.1:p.Glu429Ala chr1:11854476 4524 XM_005263462.1 Transcript 1286 FMF-248 1 MODERATE - -1 - SNV EntrezGene - protein_coding - - - XP_005263519.1 - - - - - tolerated(0.14) benign(0.021) - 0.2494 0.1513 0.1513 0.2192 0.3131 0.4172 0.155 0.3131 0.289 0.1582 0.1594 0.2941 0.2198 0.3194 0.3186 0.2963 0.4116 - 1,1 - - 1249 0.2494009584664537 200 0.15128593040847202 105 0.15129682997118155 221 0.21924603174603174 315 0.31312127236580517 408 0.4171779141104294 1207 0.3131811105345096 ./. T 19.89 2.566020 0.36960 0.43665 0.98646129547053563 ./. 683 0.15501588742623695 2693 0.3131395348837209 2.162203 -0.0608863915964679 0.37161 2.001115 -0.156808186744175 c 1651 1.588e-01 1800 1.555e-01 35805 2.950e-01 1857 2.148e-01 2069 3.128e-01 21297 3.191e-01 6855 4.153e-01 31308 2.948e-01 1429 1.578e-01 1733 1.546e-01 31308 2.949e-01 1685 2.145e-01 2069 3.128e-01 17354 3.193e-01 6818 4.157e-01 25932 2.857e-01 1648 1.588e-01 1795 1.552e-01 25930 2.858e-01 1170 2.075e-01 1200 3.156e-01 13045 3.096e-01 6851 4.153e-01 0.73639 T,T,T,T -0.78,-0.78,-0.78,-0.78 4.74 4.74 0.59564 0 0.702456 0.74369 ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000011021.17&ENSG00000177000.6&ENSG00000177000.6&ENSG00000242349.1&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000011021.17&ENSG00000242349.1&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000011021.17&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000011021.17&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6 Adipose_Subcutaneous&Adipose_Visceral_Omentum&Artery_Aorta&Artery_Tibial&Artery_Tibial&Brain_Caudate_basal_ganglia&Brain_Cerebellum&Brain_Cerebellum&Brain_Cortex&Brain_Nucleus_accumbens_basal_ganglia&Breast_Mammary_Tissue&Cells_Transformed_fibroblasts&Cells_Transformed_fibroblasts&Cells_Transformed_fibroblasts&Colon_Sigmoid&Colon_Transverse&Esophagus_Mucosa&Esophagus_Muscularis&Esophagus_Muscularis&Lung&Muscle_Skeletal&Nerve_Tibial&Pancreas&Skin_Not_Sun_Exposed_Suprapubic&Skin_Not_Sun_Exposed_Suprapubic&Skin_Sun_Exposed_Lower_leg&Thyroid&Whole_Blood 0.99999999932141 0.74713 0 0.743671 0.96052 2&6&3&2 0&3&1&1 0 0.714379 0.83238 0.095160 0.62918 D 0.000001 - - - T 0.00011 0.0000 T 0.08152 -1.0759 - - - - - MTHR_HUMAN L 1.45 0.36831 E429A E470A,E470A,E429A,E429A 0.58814 simple_aae,simple_aae,simple_aae,simple_aae P,P,P,P 1.65022e-06,1.65022e-06,1.65022e-06,1.65022e-06 0.63397 D -3.09 B,P 0.34532 0.021,0.462 B 0.25850 0.009,0.065 0.48422 0.197 9 0.30473 T 0.1,0.135,0.1,0.135 13.7416 0.62174 0.0:0.0:0.0:1.0 1205 0.3249730312837109 ENST00000376583,ENST00000376585,ENST00000376592,NM_005957.4,ENST00000376590 E470A,E470A,E429A,E429A,E429A 429,470 P42898,Q5SNW6 MTHR_HUMAN,. 0.45614 0.391,0.387,0.391,0.391,0.397 A 429,470,429,470 E G - 1 0 2 AEFDBCI D 0.67133 0.96060 MTHFR 2417 1.579326e-01 15304 5373 1.600060e-01 33580 246250 2906 2.950254e-01 9850 3780 2.191813e-01 17246 7139 3.201632e-01 22298 35620 3.188728e-01 111706 1565 2.853756e-01 5484 12658 4.112143e-01 30782 1445 1.663214e-01 8688 154 1.837709e-01 838 30854 87 2.880795e-01 302 364 2.255266e-01 1614 1079 3.089920e-01 3492 4593 3.074297e-01 14940 268 2.734694e-01 980 0 0.732398 0.92378 0.968000 0.33884 0.914000 0.39028 3.756000 0.54670 1.061000 0.80716 11794419 T GAA neutral chr1_11854476_T/G - 1532 T G 347 E/A gAa/gCa MTHFR 8/12 - HET missense_variant uncertain_significance,benign,likely_benign,other,risk_factor rs1801131,CM981315 rs1801131 - - - - - rs1801131 MTHFR deficiency, thermolabile type&fluorouracil, leucovorin, and oxaliplatin response - Efficacy&Neural tube defects, folate-sensitive&not specified - - 1 11777063 1 11854476 35807 2.949e-01 71458 2.901848e-01 7990 2.589616e-01 ENSG00000177000 ENSP00000365777,ENSP00000365767,ENSP00000365775,ENSP00000365770 ENST00000376592,ENST00000376583,ENST00000376590,ENST00000376585 XM_005263463.1:c.1040A>C XP_005263520.1:p.Glu347Ala chr1:11854476 4524 XM_005263463.1 Transcript 1040 FMF-248 1 MODERATE - -1 - SNV EntrezGene - protein_coding - - - XP_005263520.1 - - - - - - - - 0.2494 0.1513 0.1513 0.2192 0.3131 0.4172 0.155 0.3131 0.289 0.1582 0.1594 0.2941 0.2198 0.3194 0.3186 0.2963 0.4116 - 1,1 - - 1249 0.2494009584664537 200 0.15128593040847202 105 0.15129682997118155 221 0.21924603174603174 315 0.31312127236580517 408 0.4171779141104294 1207 0.3131811105345096 ./. T 19.89 2.566020 0.36960 0.43665 0.98646129547053563 ./. 683 0.15501588742623695 2693 0.3131395348837209 2.162203 -0.0608863915964679 0.37161 2.001115 -0.156808186744175 c 1651 1.588e-01 1800 1.555e-01 35805 2.950e-01 1857 2.148e-01 2069 3.128e-01 21297 3.191e-01 6855 4.153e-01 31308 2.948e-01 1429 1.578e-01 1733 1.546e-01 31308 2.949e-01 1685 2.145e-01 2069 3.128e-01 17354 3.193e-01 6818 4.157e-01 25932 2.857e-01 1648 1.588e-01 1795 1.552e-01 25930 2.858e-01 1170 2.075e-01 1200 3.156e-01 13045 3.096e-01 6851 4.153e-01 0.73639 T,T,T,T -0.78,-0.78,-0.78,-0.78 4.74 4.74 0.59564 0 0.702456 0.74369 ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000011021.17&ENSG00000177000.6&ENSG00000177000.6&ENSG00000242349.1&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000011021.17&ENSG00000242349.1&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000011021.17&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6&ENSG00000011021.17&ENSG00000177000.6&ENSG00000177000.6&ENSG00000177000.6 Adipose_Subcutaneous&Adipose_Visceral_Omentum&Artery_Aorta&Artery_Tibial&Artery_Tibial&Brain_Caudate_basal_ganglia&Brain_Cerebellum&Brain_Cerebellum&Brain_Cortex&Brain_Nucleus_accumbens_basal_ganglia&Breast_Mammary_Tissue&Cells_Transformed_fibroblasts&Cells_Transformed_fibroblasts&Cells_Transformed_fibroblasts&Colon_Sigmoid&Colon_Transverse&Esophagus_Mucosa&Esophagus_Muscularis&Esophagus_Muscularis&Lung&Muscle_Skeletal&Nerve_Tibial&Pancreas&Skin_Not_Sun_Exposed_Suprapubic&Skin_Not_Sun_Exposed_Suprapubic&Skin_Sun_Exposed_Lower_leg&Thyroid&Whole_Blood 0.99999999932141 0.74713 0 0.743671 0.96052 2&6&3&2 0&3&1&1 0 0.714379 0.83238 0.095160 0.62918 D 0.000001 - - - T 0.00011 0.0000 T 0.08152 -1.0759 - - - - - MTHR_HUMAN L 1.45 0.36831 E429A E470A,E470A,E429A,E429A 0.58814 simple_aae,simple_aae,simple_aae,simple_aae P,P,P,P 1.65022e-06,1.65022e-06,1.65022e-06,1.65022e-06 0.63397 D -3.09 B,P 0.34532 0.021,0.462 B 0.25850 0.009,0.065 0.48422 0.197 9 0.30473 T 0.1,0.135,0.1,0.135 13.7416 0.62174 0.0:0.0:0.0:1.0 1205 0.3249730312837109 ENST00000376583,ENST00000376585,ENST00000376592,NM_005957.4,ENST00000376590 E470A,E470A,E429A,E429A,E429A 429,470 P42898,Q5SNW6 MTHR_HUMAN,. 0.45614 0.391,0.387,0.391,0.391,0.397 A 429,470,429,470 E G - 1 0 2 AEFDBCI D 0.67133 0.96060 MTHFR 2417 1.579326e-01 15304 5373 1.600060e-01 33580 246250 2906 2.950254e-01 9850 3780 2.191813e-01 17246 7139 3.201632e-01 22298 35620 3.188728e-01 111706 1565 2.853756e-01 5484 12658 4.112143e-01 30782 1445 1.663214e-01 8688 154 1.837709e-01 838 30854 87 2.880795e-01 302 364 2.255266e-01 1614 1079 3.089920e-01 3492 4593 3.074297e-01 14940 268 2.734694e-01 980 0 0.732398 0.92378 0.968000 0.33884 0.914000 0.39028 3.756000 0.54670 1.061000 0.80716 11794419 T GAA - chr1_11856378_G/A - 951 G A 263 A/V gCc/gTc MTHFR 5/12 - HET missense_variant uncertain_significance,not_provided,benign,likely_benign,drug_response,other rs1801133,CM950819 rs1801133 - - - MTHFR:A222V,MTHFR:A263V 95|519|2242 rs1801133 cyclophosphamide response - Toxicity/ADR&carboplatin response - Efficacy&Neural tube defects, folate-sensitive&methotrexate response - Dosage, Efficacy, Toxicity/ADR&not specified - FAD-linked oxidoreductase-like 1 11778965 1 11856378 36865 3.036e-01 77385 3.142538e-01 7944 2.572372e-01 ENSG00000177000 ENSP00000365777,ENSP00000365767,ENSP00000365775,ENSP00000365770 ENST00000376592,ENST00000376583,ENST00000376590,ENST00000376585 NM_001330358.1:c.788C>T NP_001317287.1:p.Ala263Val chr1:11856378 4524 NM_001330358.1 Transcript 788 FMF-248 1 MODERATE - -1 - SNV EntrezGene - protein_coding YES - - NP_001317287.1 - - - rseq_mrna_match - deleterious(0.02) probably_damaging(0.999) - 0.2454 0.09 0.4741 0.2956 0.3648 0.1186 0.1217 0.3469 0.3149 0.1076 0.5027 0.4569 0.2905 0.2307 0.3396 0.3297 0.1451 - 1,1 - - 1229 0.2454073482428115 119 0.09001512859304085 329 0.47406340057636887 298 0.29563492063492064 367 0.3648111332007952 116 0.11860940695296524 1288 0.3341982355993773 G/G G 25.0 4.913833 0.66032 0.99483 0.99932935611446583 G/G 536 0.12165229232864276 2983 0.34686046511627905 7.03449 0.658031175169578 0.79087 7.694628 0.738594523497477 c 1169 1.124e-01 5952 5.141e-01 36864 3.037e-01 2640 3.052e-01 1473 2.227e-01 23025 3.450e-01 2327 1.409e-01 31996 3.013e-01 1006 1.110e-01 5799 5.170e-01 31996 3.013e-01 2451 3.118e-01 1473 2.227e-01 18746 3.449e-01 2309 1.407e-01 28129 3.100e-01 1165 1.122e-01 5946 5.141e-01 28128 3.100e-01 1839 3.262e-01 868 2.283e-01 15762 3.741e-01 2324 1.408e-01 0.96438 D,D,D,D -4.03,-4.03,-4.03,-4.03 5.08 5.08 0.68249 0 0.702456 0.74369 ENSG00000242349.1&ENSG00000242349.1&ENSG00000242349.1&ENSG00000242349.1&ENSG00000242349.1&ENSG00000242349.1&ENSG00000177000.6&ENSG00000242349.1&ENSG00000177000.6&ENSG00000116688.12 Adipose_Subcutaneous&Artery_Tibial&Brain_Cerebellum&Cells_Transformed_fibroblasts&Lung&Muscle_Skeletal&Skin_Sun_Exposed_Lower_leg&Skin_Sun_Exposed_Lower_leg&Thyroid&Whole_Blood 1.0 0.98309 0 0.724815 0.87840 6&6&3&6&2 3&3&1&3&1 0 0.735409 0.98420 0.047442 0.84324 D 0.000000 - - - T 0.00011 0.0000 T 0.00000 -1.4547 - - - - - MTHR_HUMAN M 2.965 0.85452 A222V A263V,A263V,A222V,A222V 0.58814 simple_aae,simple_aae,simple_aae,simple_aae P,P,P,P 8.64474e-08,8.64474e-08,8.64474e-08,8.64474e-08 0.71232 D -3.76 D 0.76378 0.998,0.999 D 0.75945 0.941,0.987 0.95136 0.842 9 0.72092 D 0.002,0.027,0.002,0.027 17.4321 0.87376 0.0:0.0:1.0:0.0 1224 0.3300970873786408 ENST00000376583,ENST00000376585,ENST00000376592,NM_005957.4,ENST00000376590 A263V,A263V,A222V,A222V,A222V 222,263 P42898,Q5SNW6 MTHR_HUMAN,. 0.95211 0.955,0.953,0.955,0.955,0.955 V 222,263,222,263 A A - 1 0 2 ALL D 0.78324 0.97964 MTHFR 1615 1.055280e-01 15304 16896 5.031267e-01 33582 246250 4503 4.571574e-01 9850 5066 2.937152e-01 17248 5128 2.299964e-01 22296 37947 3.397164e-01 111702 1785 3.253737e-01 5486 4445 1.444026e-01 30782 988 1.131470e-01 8732 406 4.844869e-01 838 30882 135 4.470199e-01 302 462 2.866005e-01 1612 820 2.350917e-01 3488 4876 3.265033e-01 14934 257 2.633197e-01 976 0 0.722319 0.85350 1.000000 0.71511 0.530000 0.27592 9.137000 0.93717 1.048000 0.71291 11796321 G GCC deleterious chr1_11856378_G/A - 894 G A 222 A/V gCc/gTc MTHFR 5/12 - HET missense_variant uncertain_significance,not_provided,benign,likely_benign,drug_response,other rs1801133,CM950819 rs1801133 - - - MTHFR:A222V,MTHFR:A263V 95|519|2242 rs1801133 cyclophosphamide response - Toxicity/ADR&carboplatin response - Efficacy&Neural tube defects, folate-sensitive&methotrexate response - Dosage, Efficacy, Toxicity/ADR&not specified - FAD-linked oxidoreductase-like 1 11778965 1 11856378 36865 3.036e-01 77385 3.142538e-01 7944 2.572372e-01 ENSG00000177000 ENSP00000365777,ENSP00000365767,ENSP00000365775,ENSP00000365770 ENST00000376592,ENST00000376583,ENST00000376590,ENST00000376585 NM_005957.4:c.665C>T NP_005948.3:p.Ala222Val chr1:11856378 4524 NM_005957.4 Transcript 665 FMF-248 1 MODERATE - -1 - SNV EntrezGene - protein_coding - - - NP_005948.3 - - - - - deleterious(0) probably_damaging(0.998) - 0.2454 0.09 0.4741 0.2956 0.3648 0.1186 0.1217 0.3469 0.3149 0.1076 0.5027 0.4569 0.2905 0.2307 0.3396 0.3297 0.1451 - 1,1 - - 1229 0.2454073482428115 119 0.09001512859304085 329 0.47406340057636887 298 0.29563492063492064 367 0.3648111332007952 116 0.11860940695296524 1288 0.3341982355993773 G/G G 25.0 4.913833 0.66032 0.99483 0.99932935611446583 G/G 536 0.12165229232864276 2983 0.34686046511627905 7.03449 0.658031175169578 0.79087 7.694628 0.738594523497477 c 1169 1.124e-01 5952 5.141e-01 36864 3.037e-01 2640 3.052e-01 1473 2.227e-01 23025 3.450e-01 2327 1.409e-01 31996 3.013e-01 1006 1.110e-01 5799 5.170e-01 31996 3.013e-01 2451 3.118e-01 1473 2.227e-01 18746 3.449e-01 2309 1.407e-01 28129 3.100e-01 1165 1.122e-01 5946 5.141e-01 28128 3.100e-01 1839 3.262e-01 868 2.283e-01 15762 3.741e-01 2324 1.408e-01 0.96438 D,D,D,D -4.03,-4.03,-4.03,-4.03 5.08 5.08 0.68249 0 0.702456 0.74369 ENSG00000242349.1&ENSG00000242349.1&ENSG00000242349.1&ENSG00000242349.1&ENSG00000242349.1&ENSG00000242349.1&ENSG00000177000.6&ENSG00000242349.1&ENSG00000177000.6&ENSG00000116688.12 Adipose_Subcutaneous&Artery_Tibial&Brain_Cerebellum&Cells_Transformed_fibroblasts&Lung&Muscle_Skeletal&Skin_Sun_Exposed_Lower_leg&Skin_Sun_Exposed_Lower_leg&Thyroid&Whole_Blood 1.0 0.98309 0 0.724815 0.87840 6&6&3&6&2 3&3&1&3&1 0 0.735409 0.98420 0.047442 0.84324 D 0.000000 - - - T 0.00011 0.0000 T 0.00000 -1.4547 - - - - - MTHR_HUMAN M 2.965 0.85452 A222V A263V,A263V,A222V,A222V 0.58814 simple_aae,simple_aae,simple_aae,simple_aae P,P,P,P 8.64474e-08,8.64474e-08,8.64474e-08,8.64474e-08 0.71232 D -3.76 D 0.76378 0.998,0.999 D 0.75945 0.941,0.987 0.95136 0.842 9 0.72092 D 0.002,0.027,0.002,0.027 17.4321 0.87376 0.0:0.0:1.0:0.0 1224 0.3300970873786408 ENST00000376583,ENST00000376585,ENST00000376592,NM_005957.4,ENST00000376590 A263V,A263V,A222V,A222V,A222V 222,263 P42898,Q5SNW6 MTHR_HUMAN,. 0.95211 0.955,0.953,0.955,0.955,0.955 V 222,263,222,263 A A - 1 0 2 ALL D 0.78324 0.97964 MTHFR 1615 1.055280e-01 15304 16896 5.031267e-01 33582 246250 4503 4.571574e-01 9850 5066 2.937152e-01 17248 5128 2.299964e-01 22296 37947 3.397164e-01 111702 1785 3.253737e-01 5486 4445 1.444026e-01 30782 988 1.131470e-01 8732 406 4.844869e-01 838 30882 135 4.470199e-01 302 462 2.866005e-01 1612 820 2.350917e-01 3488 4876 3.265033e-01 14934 257 2.633197e-01 976 0 0.722319 0.85350 1.000000 0.71511 0.530000 0.27592 9.137000 0.93717 1.048000 0.71291 11796321 G GCC deleterious chr1_11856378_G/A - 1731 G A 263 A/V gCc/gTc MTHFR 5/12 - HET missense_variant uncertain_significance,not_provided,benign,likely_benign,drug_response,other rs1801133,CM950819 rs1801133 - - - MTHFR:A222V,MTHFR:A263V 95|519|2242 rs1801133 cyclophosphamide response - Toxicity/ADR&carboplatin response - Efficacy&Neural tube defects, folate-sensitive&methotrexate response - Dosage, Efficacy, Toxicity/ADR&not specified - FAD-linked oxidoreductase-like 1 11778965 1 11856378 36865 3.036e-01 77385 3.142538e-01 7944 2.572372e-01 ENSG00000177000 ENSP00000365777,ENSP00000365767,ENSP00000365775,ENSP00000365770 ENST00000376592,ENST00000376583,ENST00000376590,ENST00000376585 XM_005263458.1:c.788C>T XP_005263515.1:p.Ala263Val chr1:11856378 4524 XM_005263458.1 Transcript 788 FMF-248 1 MODERATE - -1 - SNV EntrezGene - protein_coding YES - - XP_005263515.1 - - - - - deleterious(0.02) probably_damaging(0.999) - 0.2454 0.09 0.4741 0.2956 0.3648 0.1186 0.1217 0.3469 0.3149 0.1076 0.5027 0.4569 0.2905 0.2307 0.3396 0.3297 0.1451 - 1,1 - - 1229 0.2454073482428115 119 0.09001512859304085 329 0.47406340057636887 298 0.29563492063492064 367 0.3648111332007952 116 0.11860940695296524 1288 0.3341982355993773 G/G G 25.0 4.913833 0.66032 0.99483 0.99932935611446583 G/G 536 0.12165229232864276 2983 0.34686046511627905 7.03449 0.658031175169578 0.79087 7.694628 0.738594523497477 c 1169 1.124e-01 5952 5.141e-01 36864 3.037e-01 2640 3.052e-01 1473 2.227e-01 23025 3.450e-01 2327 1.409e-01 31996 3.013e-01 1006 1.110e-01 5799 5.170e-01 31996 3.013e-01 2451 3.118e-01 1473 2.227e-01 18746 3.449e-01 2309 1.407e-01 28129 3.100e-01 1165 1.122e-01 5946 5.141e-01 28128 3.100e-01 1839 3.262e-01 868 2.283e-01 15762 3.741e-01 2324 1.408e-01 0.96438 D,D,D,D -4.03,-4.03,-4.03,-4.03 5.08 5.08 0.68249 0 0.702456 0.74369 ENSG00000242349.1&ENSG00000242349.1&ENSG00000242349.1&ENSG00000242349.1&ENSG00000242349.1&ENSG00000242349.1&ENSG00000177000.6&ENSG00000242349.1&ENSG00000177000.6&ENSG00000116688.12 Adipose_Subcutaneous&Artery_Tibial&Brain_Cerebellum&Cells_Transformed_fibroblasts&Lung&Muscle_Skeletal&Skin_Sun_Exposed_Lower_leg&Skin_Sun_Exposed_Lower_leg&Thyroid&Whole_Blood 1.0 0.98309 0 0.724815 0.87840 6&6&3&6&2 3&3&1&3&1 0 0.735409 0.98420 0.047442 0.84324 D 0.000000 - - - T 0.00011 0.0000 T 0.00000 -1.4547 - - - - - MTHR_HUMAN M 2.965 0.85452 A222V A263V,A263V,A222V,A222V 0.58814 simple_aae,simple_aae,simple_aae,simple_aae P,P,P,P 8.64474e-08,8.64474e-08,8.64474e-08,8.64474e-08 0.71232 D -3.76 D 0.76378 0.998,0.999 D 0.75945 0.941,0.987 0.95136 0.842 9 0.72092 D 0.002,0.027,0.002,0.027 17.4321 0.87376 0.0:0.0:1.0:0.0 1224 0.3300970873786408 ENST00000376583,ENST00000376585,ENST00000376592,NM_005957.4,ENST00000376590 A263V,A263V,A222V,A222V,A222V 222,263 P42898,Q5SNW6 MTHR_HUMAN,. 0.95211 0.955,0.953,0.955,0.955,0.955 V 222,263,222,263 A A - 1 0 2 ALL D 0.78324 0.97964 MTHFR 1615 1.055280e-01 15304 16896 5.031267e-01 33582 246250 4503 4.571574e-01 9850 5066 2.937152e-01 17248 5128 2.299964e-01 22296 37947 3.397164e-01 111702 1785 3.253737e-01 5486 4445 1.444026e-01 30782 988 1.131470e-01 8732 406 4.844869e-01 838 30882 135 4.470199e-01 302 462 2.866005e-01 1612 820 2.350917e-01 3488 4876 3.265033e-01 14934 257 2.633197e-01 976 0 0.722319 0.85350 1.000000 0.71511 0.530000 0.27592 9.137000 0.93717 1.048000 0.71291 11796321 G GCC deleterious chr1_11856378_G/A - 2006 G A 245 A/V gCc/gTc MTHFR 4/11 - HET missense_variant uncertain_significance,not_provided,benign,likely_benign,drug_response,other rs1801133,CM950819 rs1801133 - - - - - rs1801133 cyclophosphamide response - Toxicity/ADR&carboplatin response - Efficacy&Neural tube defects, folate-sensitive&methotrexate response - Dosage, Efficacy, Toxicity/ADR&not specified - FAD-linked oxidoreductase-like 1 11778965 1 11856378 36865 3.036e-01 77385 3.142538e-01 7944 2.572372e-01 ENSG00000177000 ENSP00000365777,ENSP00000365767,ENSP00000365775,ENSP00000365770 ENST00000376592,ENST00000376583,ENST00000376590,ENST00000376585 XM_005263459.1:c.734C>T XP_005263516.1:p.Ala245Val chr1:11856378 4524 XM_005263459.1 Transcript 734 FMF-248 1 MODERATE - -1 - SNV EntrezGene - protein_coding - - - XP_005263516.1 - - - - - - - - 0.2454 0.09 0.4741 0.2956 0.3648 0.1186 0.1217 0.3469 0.3149 0.1076 0.5027 0.4569 0.2905 0.2307 0.3396 0.3297 0.1451 - 1,1 - - 1229 0.2454073482428115 119 0.09001512859304085 329 0.47406340057636887 298 0.29563492063492064 367 0.3648111332007952 116 0.11860940695296524 1288 0.3341982355993773 G/G G 25.0 4.913833 0.66032 0.99483 0.99932935611446583 G/G 536 0.12165229232864276 2983 0.34686046511627905 7.03449 0.658031175169578 0.79087 7.694628 0.738594523497477 c 1169 1.124e-01 5952 5.141e-01 36864 3.037e-01 2640 3.052e-01 1473 2.227e-01 23025 3.450e-01 2327 1.409e-01 31996 3.013e-01 1006 1.110e-01 5799 5.170e-01 31996 3.013e-01 2451 3.118e-01 1473 2.227e-01 18746 3.449e-01 2309 1.407e-01 28129 3.100e-01 1165 1.122e-01 5946 5.141e-01 28128 3.100e-01 1839 3.262e-01 868 2.283e-01 15762 3.741e-01 2324 1.408e-01 0.96438 D,D,D,D -4.03,-4.03,-4.03,-4.03 5.08 5.08 0.68249 0 0.702456 0.74369 ENSG00000242349.1&ENSG00000242349.1&ENSG00000242349.1&ENSG00000242349.1&ENSG00000242349.1&ENSG00000242349.1&ENSG00000177000.6&ENSG00000242349.1&ENSG00000177000.6&ENSG00000116688.12 Adipose_Subcutaneous&Artery_Tibial&Brain_Cerebellum&Cells_Transformed_fibroblasts&Lung&Muscle_Skeletal&Skin_Sun_Exposed_Lower_leg&Skin_Sun_Exposed_Lower_leg&Thyroid&Whole_Blood 1.0 0.98309 0 0.724815 0.87840 6&6&3&6&2 3&3&1&3&1 0 0.735409 0.98420 0.047442 0.84324 D 0.000000 - - - T 0.00011 0.0000 T 0.00000 -1.4547 - - - - - MTHR_HUMAN M 2.965 0.85452 A222V A263V,A263V,A222V,A222V 0.58814 simple_aae,simple_aae,simple_aae,simple_aae P,P,P,P 8.64474e-08,8.64474e-08,8.64474e-08,8.64474e-08 0.71232 D -3.76 D 0.76378 0.998,0.999 D 0.75945 0.941,0.987 0.95136 0.842 9 0.72092 D 0.002,0.027,0.002,0.027 17.4321 0.87376 0.0:0.0:1.0:0.0 1224 0.3300970873786408 ENST00000376583,ENST00000376585,ENST00000376592,NM_005957.4,ENST00000376590 A263V,A263V,A222V,A222V,A222V 222,263 P42898,Q5SNW6 MTHR_HUMAN,. 0.95211 0.955,0.953,0.955,0.955,0.955 V 222,263,222,263 A A - 1 0 2 ALL D 0.78324 0.97964 MTHFR 1615 1.055280e-01 15304 16896 5.031267e-01 33582 246250 4503 4.571574e-01 9850 5066 2.937152e-01 17248 5128 2.299964e-01 22296 37947 3.397164e-01 111702 1785 3.253737e-01 5486 4445 1.444026e-01 30782 988 1.131470e-01 8732 406 4.844869e-01 838 30882 135 4.470199e-01 302 462 2.866005e-01 1612 820 2.350917e-01 3488 4876 3.265033e-01 14934 257 2.633197e-01 976 0 0.722319 0.85350 1.000000 0.71511 0.530000 0.27592 9.137000 0.93717 1.048000 0.71291 11796321 G GCC - chr1_11856378_G/A - 1333 G A 222 A/V gCc/gTc MTHFR 5/12 - HET missense_variant uncertain_significance,not_provided,benign,likely_benign,drug_response,other rs1801133,CM950819 rs1801133 - - - MTHFR:A222V,MTHFR:A263V 95|519|2242 rs1801133 cyclophosphamide response - Toxicity/ADR&carboplatin response - Efficacy&Neural tube defects, folate-sensitive&methotrexate response - Dosage, Efficacy, Toxicity/ADR&not specified - FAD-linked oxidoreductase-like 1 11778965 1 11856378 36865 3.036e-01 77385 3.142538e-01 7944 2.572372e-01 ENSG00000177000 ENSP00000365777,ENSP00000365767,ENSP00000365775,ENSP00000365770 ENST00000376592,ENST00000376583,ENST00000376590,ENST00000376585 XM_005263460.1:c.665C>T XP_005263517.1:p.Ala222Val chr1:11856378 4524 XM_005263460.1 Transcript 665 FMF-248 1 MODERATE - -1 - SNV EntrezGene - protein_coding - - - XP_005263517.1 - - - - - deleterious(0) probably_damaging(0.998) - 0.2454 0.09 0.4741 0.2956 0.3648 0.1186 0.1217 0.3469 0.3149 0.1076 0.5027 0.4569 0.2905 0.2307 0.3396 0.3297 0.1451 - 1,1 - - 1229 0.2454073482428115 119 0.09001512859304085 329 0.47406340057636887 298 0.29563492063492064 367 0.3648111332007952 116 0.11860940695296524 1288 0.3341982355993773 G/G G 25.0 4.913833 0.66032 0.99483 0.99932935611446583 G/G 536 0.12165229232864276 2983 0.34686046511627905 7.03449 0.658031175169578 0.79087 7.694628 0.738594523497477 c 1169 1.124e-01 5952 5.141e-01 36864 3.037e-01 2640 3.052e-01 1473 2.227e-01 23025 3.450e-01 2327 1.409e-01 31996 3.013e-01 1006 1.110e-01 5799 5.170e-01 31996 3.013e-01 2451 3.118e-01 1473 2.227e-01 18746 3.449e-01 2309 1.407e-01 28129 3.100e-01 1165 1.122e-01 5946 5.141e-01 28128 3.100e-01 1839 3.262e-01 868 2.283e-01 15762 3.741e-01 2324 1.408e-01 0.96438 D,D,D,D -4.03,-4.03,-4.03,-4.03 5.08 5.08 0.68249 0 0.702456 0.74369 ENSG00000242349.1&ENSG00000242349.1&ENSG00000242349.1&ENSG00000242349.1&ENSG00000242349.1&ENSG00000242349.1&ENSG00000177000.6&ENSG00000242349.1&ENSG00000177000.6&ENSG00000116688.12 Adipose_Subcutaneous&Artery_Tibial&Brain_Cerebellum&Cells_Transformed_fibroblasts&Lung&Muscle_Skeletal&Skin_Sun_Exposed_Lower_leg&Skin_Sun_Exposed_Lower_leg&Thyroid&Whole_Blood 1.0 0.98309 0 0.724815 0.87840 6&6&3&6&2 3&3&1&3&1 0 0.735409 0.98420 0.047442 0.84324 D 0.000000 - - - T 0.00011 0.0000 T 0.00000 -1.4547 - - - - - MTHR_HUMAN M 2.965 0.85452 A222V A263V,A263V,A222V,A222V 0.58814 simple_aae,simple_aae,simple_aae,simple_aae P,P,P,P 8.64474e-08,8.64474e-08,8.64474e-08,8.64474e-08 0.71232 D -3.76 D 0.76378 0.998,0.999 D 0.75945 0.941,0.987 0.95136 0.842 9 0.72092 D 0.002,0.027,0.002,0.027 17.4321 0.87376 0.0:0.0:1.0:0.0 1224 0.3300970873786408 ENST00000376583,ENST00000376585,ENST00000376592,NM_005957.4,ENST00000376590 A263V,A263V,A222V,A222V,A222V 222,263 P42898,Q5SNW6 MTHR_HUMAN,. 0.95211 0.955,0.953,0.955,0.955,0.955 V 222,263,222,263 A A - 1 0 2 ALL D 0.78324 0.97964 MTHFR 1615 1.055280e-01 15304 16896 5.031267e-01 33582 246250 4503 4.571574e-01 9850 5066 2.937152e-01 17248 5128 2.299964e-01 22296 37947 3.397164e-01 111702 1785 3.253737e-01 5486 4445 1.444026e-01 30782 988 1.131470e-01 8732 406 4.844869e-01 838 30882 135 4.470199e-01 302 462 2.866005e-01 1612 820 2.350917e-01 3488 4876 3.265033e-01 14934 257 2.633197e-01 976 0 0.722319 0.85350 1.000000 0.71511 0.530000 0.27592 9.137000 0.93717 1.048000 0.71291 11796321 G GCC deleterious chr1_11856378_G/A - 1229 G A 222 A/V gCc/gTc MTHFR 5/12 - HET missense_variant uncertain_significance,not_provided,benign,likely_benign,drug_response,other rs1801133,CM950819 rs1801133 - - - MTHFR:A222V,MTHFR:A263V 95|519|2242 rs1801133 cyclophosphamide response - Toxicity/ADR&carboplatin response - Efficacy&Neural tube defects, folate-sensitive&methotrexate response - Dosage, Efficacy, Toxicity/ADR&not specified - FAD-linked oxidoreductase-like 1 11778965 1 11856378 36865 3.036e-01 77385 3.142538e-01 7944 2.572372e-01 ENSG00000177000 ENSP00000365777,ENSP00000365767,ENSP00000365775,ENSP00000365770 ENST00000376592,ENST00000376583,ENST00000376590,ENST00000376585 XM_005263461.1:c.665C>T XP_005263518.1:p.Ala222Val chr1:11856378 4524 XM_005263461.1 Transcript 665 FMF-248 1 MODERATE - -1 - SNV EntrezGene - protein_coding - - - XP_005263518.1 - - - - - deleterious(0) probably_damaging(0.998) - 0.2454 0.09 0.4741 0.2956 0.3648 0.1186 0.1217 0.3469 0.3149 0.1076 0.5027 0.4569 0.2905 0.2307 0.3396 0.3297 0.1451 - 1,1 - - 1229 0.2454073482428115 119 0.09001512859304085 329 0.47406340057636887 298 0.29563492063492064 367 0.3648111332007952 116 0.11860940695296524 1288 0.3341982355993773 G/G G 25.0 4.913833 0.66032 0.99483 0.99932935611446583 G/G 536 0.12165229232864276 2983 0.34686046511627905 7.03449 0.658031175169578 0.79087 7.694628 0.738594523497477 c 1169 1.124e-01 5952 5.141e-01 36864 3.037e-01 2640 3.052e-01 1473 2.227e-01 23025 3.450e-01 2327 1.409e-01 31996 3.013e-01 1006 1.110e-01 5799 5.170e-01 31996 3.013e-01 2451 3.118e-01 1473 2.227e-01 18746 3.449e-01 2309 1.407e-01 28129 3.100e-01 1165 1.122e-01 5946 5.141e-01 28128 3.100e-01 1839 3.262e-01 868 2.283e-01 15762 3.741e-01 2324 1.408e-01 0.96438 D,D,D,D -4.03,-4.03,-4.03,-4.03 5.08 5.08 0.68249 0 0.702456 0.74369 ENSG00000242349.1&ENSG00000242349.1&ENSG00000242349.1&ENSG00000242349.1&ENSG00000242349.1&ENSG00000242349.1&ENSG00000177000.6&ENSG00000242349.1&ENSG00000177000.6&ENSG00000116688.12 Adipose_Subcutaneous&Artery_Tibial&Brain_Cerebellum&Cells_Transformed_fibroblasts&Lung&Muscle_Skeletal&Skin_Sun_Exposed_Lower_leg&Skin_Sun_Exposed_Lower_leg&Thyroid&Whole_Blood 1.0 0.98309 0 0.724815 0.87840 6&6&3&6&2 3&3&1&3&1 0 0.735409 0.98420 0.047442 0.84324 D 0.000000 - - - T 0.00011 0.0000 T 0.00000 -1.4547 - - - - - MTHR_HUMAN M 2.965 0.85452 A222V A263V,A263V,A222V,A222V 0.58814 simple_aae,simple_aae,simple_aae,simple_aae P,P,P,P 8.64474e-08,8.64474e-08,8.64474e-08,8.64474e-08 0.71232 D -3.76 D 0.76378 0.998,0.999 D 0.75945 0.941,0.987 0.95136 0.842 9 0.72092 D 0.002,0.027,0.002,0.027 17.4321 0.87376 0.0:0.0:1.0:0.0 1224 0.3300970873786408 ENST00000376583,ENST00000376585,ENST00000376592,NM_005957.4,ENST00000376590 A263V,A263V,A222V,A222V,A222V 222,263 P42898,Q5SNW6 MTHR_HUMAN,. 0.95211 0.955,0.953,0.955,0.955,0.955 V 222,263,222,263 A A - 1 0 2 ALL D 0.78324 0.97964 MTHFR 1615 1.055280e-01 15304 16896 5.031267e-01 33582 246250 4503 4.571574e-01 9850 5066 2.937152e-01 17248 5128 2.299964e-01 22296 37947 3.397164e-01 111702 1785 3.253737e-01 5486 4445 1.444026e-01 30782 988 1.131470e-01 8732 406 4.844869e-01 838 30882 135 4.470199e-01 302 462 2.866005e-01 1612 820 2.350917e-01 3488 4876 3.265033e-01 14934 257 2.633197e-01 976 0 0.722319 0.85350 1.000000 0.71511 0.530000 0.27592 9.137000 0.93717 1.048000 0.71291 11796321 G GCC deleterious chr1_11856378_G/A - 696 G A 222 A/V gCc/gTc MTHFR 5/12 - HET missense_variant uncertain_significance,not_provided,benign,likely_benign,drug_response,other rs1801133,CM950819 rs1801133 - - - MTHFR:A222V,MTHFR:A263V 95|519|2242 rs1801133 cyclophosphamide response - Toxicity/ADR&carboplatin response - Efficacy&Neural tube defects, folate-sensitive&methotrexate response - Dosage, Efficacy, Toxicity/ADR&not specified - FAD-linked oxidoreductase-like 1 11778965 1 11856378 36865 3.036e-01 77385 3.142538e-01 7944 2.572372e-01 ENSG00000177000 ENSP00000365777,ENSP00000365767,ENSP00000365775,ENSP00000365770 ENST00000376592,ENST00000376583,ENST00000376590,ENST00000376585 XM_005263462.1:c.665C>T XP_005263519.1:p.Ala222Val chr1:11856378 4524 XM_005263462.1 Transcript 665 FMF-248 1 MODERATE - -1 - SNV EntrezGene - protein_coding - - - XP_005263519.1 - - - - - deleterious(0) probably_damaging(0.998) - 0.2454 0.09 0.4741 0.2956 0.3648 0.1186 0.1217 0.3469 0.3149 0.1076 0.5027 0.4569 0.2905 0.2307 0.3396 0.3297 0.1451 - 1,1 - - 1229 0.2454073482428115 119 0.09001512859304085 329 0.47406340057636887 298 0.29563492063492064 367 0.3648111332007952 116 0.11860940695296524 1288 0.3341982355993773 G/G G 25.0 4.913833 0.66032 0.99483 0.99932935611446583 G/G 536 0.12165229232864276 2983 0.34686046511627905 7.03449 0.658031175169578 0.79087 7.694628 0.738594523497477 c 1169 1.124e-01 5952 5.141e-01 36864 3.037e-01 2640 3.052e-01 1473 2.227e-01 23025 3.450e-01 2327 1.409e-01 31996 3.013e-01 1006 1.110e-01 5799 5.170e-01 31996 3.013e-01 2451 3.118e-01 1473 2.227e-01 18746 3.449e-01 2309 1.407e-01 28129 3.100e-01 1165 1.122e-01 5946 5.141e-01 28128 3.100e-01 1839 3.262e-01 868 2.283e-01 15762 3.741e-01 2324 1.408e-01 0.96438 D,D,D,D -4.03,-4.03,-4.03,-4.03 5.08 5.08 0.68249 0 0.702456 0.74369 ENSG00000242349.1&ENSG00000242349.1&ENSG00000242349.1&ENSG00000242349.1&ENSG00000242349.1&ENSG00000242349.1&ENSG00000177000.6&ENSG00000242349.1&ENSG00000177000.6&ENSG00000116688.12 Adipose_Subcutaneous&Artery_Tibial&Brain_Cerebellum&Cells_Transformed_fibroblasts&Lung&Muscle_Skeletal&Skin_Sun_Exposed_Lower_leg&Skin_Sun_Exposed_Lower_leg&Thyroid&Whole_Blood 1.0 0.98309 0 0.724815 0.87840 6&6&3&6&2 3&3&1&3&1 0 0.735409 0.98420 0.047442 0.84324 D 0.000000 - - - T 0.00011 0.0000 T 0.00000 -1.4547 - - - - - MTHR_HUMAN M 2.965 0.85452 A222V A263V,A263V,A222V,A222V 0.58814 simple_aae,simple_aae,simple_aae,simple_aae P,P,P,P 8.64474e-08,8.64474e-08,8.64474e-08,8.64474e-08 0.71232 D -3.76 D 0.76378 0.998,0.999 D 0.75945 0.941,0.987 0.95136 0.842 9 0.72092 D 0.002,0.027,0.002,0.027 17.4321 0.87376 0.0:0.0:1.0:0.0 1224 0.3300970873786408 ENST00000376583,ENST00000376585,ENST00000376592,NM_005957.4,ENST00000376590 A263V,A263V,A222V,A222V,A222V 222,263 P42898,Q5SNW6 MTHR_HUMAN,. 0.95211 0.955,0.953,0.955,0.955,0.955 V 222,263,222,263 A A - 1 0 2 ALL D 0.78324 0.97964 MTHFR 1615 1.055280e-01 15304 16896 5.031267e-01 33582 246250 4503 4.571574e-01 9850 5066 2.937152e-01 17248 5128 2.299964e-01 22296 37947 3.397164e-01 111702 1785 3.253737e-01 5486 4445 1.444026e-01 30782 988 1.131470e-01 8732 406 4.844869e-01 838 30882 135 4.470199e-01 302 462 2.866005e-01 1612 820 2.350917e-01 3488 4876 3.265033e-01 14934 257 2.633197e-01 976 0 0.722319 0.85350 1.000000 0.71511 0.530000 0.27592 9.137000 0.93717 1.048000 0.71291 11796321 G GCC deleterious chr1_11856378_G/A - 911 G A 140 A/V gCc/gTc MTHFR 5/12 - HET missense_variant uncertain_significance,not_provided,benign,likely_benign,drug_response,other rs1801133,CM950819 rs1801133 - - - - - rs1801133 cyclophosphamide response - Toxicity/ADR&carboplatin response - Efficacy&Neural tube defects, folate-sensitive&methotrexate response - Dosage, Efficacy, Toxicity/ADR&not specified - FAD-linked oxidoreductase-like 1 11778965 1 11856378 36865 3.036e-01 77385 3.142538e-01 7944 2.572372e-01 ENSG00000177000 ENSP00000365777,ENSP00000365767,ENSP00000365775,ENSP00000365770 ENST00000376592,ENST00000376583,ENST00000376590,ENST00000376585 XM_005263463.1:c.419C>T XP_005263520.1:p.Ala140Val chr1:11856378 4524 XM_005263463.1 Transcript 419 FMF-248 1 MODERATE - -1 - SNV EntrezGene - protein_coding - - - XP_005263520.1 - - - - - - - - 0.2454 0.09 0.4741 0.2956 0.3648 0.1186 0.1217 0.3469 0.3149 0.1076 0.5027 0.4569 0.2905 0.2307 0.3396 0.3297 0.1451 - 1,1 - - 1229 0.2454073482428115 119 0.09001512859304085 329 0.47406340057636887 298 0.29563492063492064 367 0.3648111332007952 116 0.11860940695296524 1288 0.3341982355993773 G/G G 25.0 4.913833 0.66032 0.99483 0.99932935611446583 G/G 536 0.12165229232864276 2983 0.34686046511627905 7.03449 0.658031175169578 0.79087 7.694628 0.738594523497477 c 1169 1.124e-01 5952 5.141e-01 36864 3.037e-01 2640 3.052e-01 1473 2.227e-01 23025 3.450e-01 2327 1.409e-01 31996 3.013e-01 1006 1.110e-01 5799 5.170e-01 31996 3.013e-01 2451 3.118e-01 1473 2.227e-01 18746 3.449e-01 2309 1.407e-01 28129 3.100e-01 1165 1.122e-01 5946 5.141e-01 28128 3.100e-01 1839 3.262e-01 868 2.283e-01 15762 3.741e-01 2324 1.408e-01 0.96438 D,D,D,D -4.03,-4.03,-4.03,-4.03 5.08 5.08 0.68249 0 0.702456 0.74369 ENSG00000242349.1&ENSG00000242349.1&ENSG00000242349.1&ENSG00000242349.1&ENSG00000242349.1&ENSG00000242349.1&ENSG00000177000.6&ENSG00000242349.1&ENSG00000177000.6&ENSG00000116688.12 Adipose_Subcutaneous&Artery_Tibial&Brain_Cerebellum&Cells_Transformed_fibroblasts&Lung&Muscle_Skeletal&Skin_Sun_Exposed_Lower_leg&Skin_Sun_Exposed_Lower_leg&Thyroid&Whole_Blood 1.0 0.98309 0 0.724815 0.87840 6&6&3&6&2 3&3&1&3&1 0 0.735409 0.98420 0.047442 0.84324 D 0.000000 - - - T 0.00011 0.0000 T 0.00000 -1.4547 - - - - - MTHR_HUMAN M 2.965 0.85452 A222V A263V,A263V,A222V,A222V 0.58814 simple_aae,simple_aae,simple_aae,simple_aae P,P,P,P 8.64474e-08,8.64474e-08,8.64474e-08,8.64474e-08 0.71232 D -3.76 D 0.76378 0.998,0.999 D 0.75945 0.941,0.987 0.95136 0.842 9 0.72092 D 0.002,0.027,0.002,0.027 17.4321 0.87376 0.0:0.0:1.0:0.0 1224 0.3300970873786408 ENST00000376583,ENST00000376585,ENST00000376592,NM_005957.4,ENST00000376590 A263V,A263V,A222V,A222V,A222V 222,263 P42898,Q5SNW6 MTHR_HUMAN,. 0.95211 0.955,0.953,0.955,0.955,0.955 V 222,263,222,263 A A - 1 0 2 ALL D 0.78324 0.97964 MTHFR 1615 1.055280e-01 15304 16896 5.031267e-01 33582 246250 4503 4.571574e-01 9850 5066 2.937152e-01 17248 5128 2.299964e-01 22296 37947 3.397164e-01 111702 1785 3.253737e-01 5486 4445 1.444026e-01 30782 988 1.131470e-01 8732 406 4.844869e-01 838 30882 135 4.470199e-01 302 462 2.866005e-01 1612 820 2.350917e-01 3488 4876 3.265033e-01 14934 257 2.633197e-01 976 0 0.722319 0.85350 1.000000 0.71511 0.530000 0.27592 9.137000 0.93717 1.048000 0.71291 11796321 G GCC - chr1_169519042_T/C - 1753 T C 536 I/M atA/atG F5 10/25 - HET missense_variant - - - - - - F5:I536M 1|1|1 - - - Cupredoxin 1 167785666 1 169519042 - - - - - - ENSG00000198734 ENSP00000356771,ENSP00000356770 ENST00000367797,ENST00000367796 NM_000130.4:c.1608A>G NP_000121.2:p.Ile536Met chr1:169519042 2153 NM_000130.4 Transcript 1608 FMF-248 1 MODERATE - -1 - SNV EntrezGene - protein_coding YES - - NP_000121.2 - - - - - tolerated(0.09) benign(0.451) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - T/T T 22.9 3.327569 0.45857 0.24300 0.94458408057769683 T/T - - - - 2.275669 -0.0250095357041435 0.38771 1.985453 -0.162063409057272 c - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 0.98509 D,D -4.99,-4.99 5.71 3.34 0.37198 0 0.547309 0.13894 - - 4.45729633684529E-4 0.07049 0 0.547309 0.14640 - - 0 0.613276 0.41441 0.396575 0.28509 N 0.014480 D 0.84938 0.171600359507 D 0.87894 0.6522 D 0.84243 0.1033 I536M Gain of disorder (P = 0.0554), Gain of MoRF binding (P = 0.1059), Loss of sheet (P = 0.1158), Gain of helix (P = 0.1736), Loss of catalytic residue at A540 (P = 0.1862) P12259 0.31105 0.327 FA5_HUMAN N 0.205 0.09372 I536M .,I536M,I536M 0.81033 without_aae,simple_aae,simple_aae D,N,N 1,0.976836,0.976836 0.40439 N -1.7 B 0.34242 0.451 B 0.30033 0.112 0.68051 0.356 9 0.12982 T 0.342,0.333 3.9597 0.08834 0.0:0.182:0.3994:0.4185 - - ENST00000367797,NM_000130.4,CCDS1281.1,ENST00000367796 I536M,I536M,I536M,I536M 536 P12259 FA5_HUMAN 0.24769 0.202,0.148,0.111,0.202 M 536 I C - 1 3 3 AEFDBI D 0.34241 0.70261 F5 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 0 0.428477 0.05869 0.999000 0.42402 0.998000 0.69722 0.494000 0.22014 1.061000 0.80716 169549804 T ATA neutral chr1_169519049_T/C - 1746 T C 534 Q/R cAa/cGa F5 10/25 - HOM missense_variant benign,pathogenic,drug_response,risk_factor rs6025,CM940389 - - - - - - - - - - - - - - - - - - - - - - - NM_000130.4:c.1601A>G NP_000121.2:p.Gln534Arg chr1:169519049 2153 NM_000130.4 Transcript 1601 FMF-248 1 MODERATE - -1 - SNV EntrezGene - protein_coding YES - - NP_000121.2 - - - - - - - - 0.994 1 0.9899 1 0.9881 0.9888 0.9957 0.9699 0.9804 0.9959 0.993 0.9815 0.9999 0.9785 0.9698 0.9825 0.9862 - 1,1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chr1_169519062_A/G - 1733 A G 530 S/P Tcc/Ccc F5 10/25 - HET missense_variant - COSM7325594 - - - - - - - - - Cupredoxin 1 167785686 1 169519062 - - - - - - ENSG00000198734 ENSP00000356771,ENSP00000356770 ENST00000367797,ENST00000367796 NM_000130.4:c.1588T>C NP_000121.2:p.Ser530Pro chr1:169519062 2153 NM_000130.4 Transcript 1588 FMF-248 1 MODERATE - -1 - SNV EntrezGene - protein_coding YES - - NP_000121.2 - - - - - deleterious(0) probably_damaging(1) - - - - - - - - - - - - - - - - - - 1 1 - - - - - - - - - - - - - - - - A/A A 28.6 6.190602 0.85423 0.95289 0.99875948933521674 A/A - - - - 7.242743 0.671011818567554 0.80038 7.520655 0.727446382327431 c - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 0.99056 D,D -5.39,-5.39 5.71 4.48 0.53808 0 0.547309 0.13894 - - 0.00204221249436426 0.09153 0 0.547309 0.14640 - - 0 0.613276 0.41441 0.242422 0.42786 D 0.000637 D 0.97152 0.659656614891 D 0.98948 0.9669 D 0.99932 1.1359 S530P Loss of catalytic residue at S530 (P = 0.0247), Gain of glycosylation at S530 (P = 0.0291), Loss of MoRF binding (P = 0.0561), Loss of phosphorylation at S530 (P = 0.0691), Loss of stability (P = 0.1075) P12259 0.61966 0.518 FA5_HUMAN M 2.98 0.85751 S530P S530P,S530P,. 0.81033 simple_aae,simple_aae,without_aae D,D,D 0.990354,0.990354,1 0.72998 D -3.91 D 0.89865 1.0 D 0.69161 0.963 0.90456 0.725 9 0.68180 D 0.003 8.7939 0.33842 0.7368:0.1497:0.0:0.1135 - - ENST00000367797,NM_000130.4,CCDS1281.1,ENST00000367796 S530P,S530P,S530P,S530P 530 P12259 FA5_HUMAN 0.62613 0.601,0.523,0.41,0.601 P 530 S G - 1 0 1 AEFBI D 0.70454 0.96734 F5 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 0 0.428477 0.05869 1.000000 0.71511 0.998000 0.69722 3.572000 0.53346 1.199000 0.96014 169549824 A TCC deleterious chr16_3293447_C/G - 2080 C G 680 M/I atG/atC MEFV 10/10 - HOM missense_variant likely_pathogenic,pathogenic rs28940580,CM970911,CM990839 rs28940580 - - - MEFV:M680I 36|711|724 rs28940580 Familial Mediterranean fever&not provided - B30.2/SPRY domain&Concanavalin A-like lectin/glucanase domain&SPRY domain 16 3233448 16 3293447 11 9.060e-05 26 1.055820e-04 - - ENSG00000103313 ENSP00000219596,ENSP00000339639,ENSP00000445079 ENST00000219596,ENST00000339854,ENST00000536379 NM_000243.2:c.2040G>C NP_000234.1:p.Met680Ile chr16:3293447 4210 NM_000243.2 Transcript 2040 FMF-248 1 MODERATE - -1 - SNV EntrezGene - protein_coding YES - - NP_000234.1 - - - - - tolerated(0.45) benign(0) - - - - - - - 0 0.0001163 0.0001034 0 0 0 0 0 0.0002286 0 0 - 1,1,1 - - - - - - - - - - - - - - - - C/C C 0.002 -1.836357 0.01032 0.05611 0.57306488083898777 C/C 0 0.0 1 1.1627906976744187E-4 0.05786653 -1.66852235618751 0.01259 0.03320854 -1.72133451108289 c 0 0 0 0 11 9.060e-05 0 0 0 0 10 1.498e-04 0 0 9 8.474e-05 0 0 0 0 9 8.474e-05 0 0 0 0 8 1.472e-04 0 0 6 6.611e-05 0 0 0 0 6 6.612e-05 0 0 0 0 6 1.424e-04 0 0 0.59195 T,T,T 0.27,0.27,0.27 5.17 -3.32 0.04636 0 0.588066 0.40457 - - 0.978585131580013 0.29892 0 0.547309 0.14640 5&5 2&1 0 0.542086 0.14228 0.394015 0.22130 N 0.061831 T 0.19152 0.00716469549083 T 0.18243 0.0424 T 0.36372 -0.9739 - - - - - MEFV_HUMAN N -0.605 0.02198 M680I M680I,M500I,M469I,. 0.08979 simple_aae,simple_aae,simple_aae,without_aae N,N,N,N 1,1,1,1 0.08988 N -0.13 B 0.02634 0.0 B 0.03956 0.001 0.67507 0.350 9 0.15433 T 0.359,0.387,0.281 5.9184 0.18187 0.0:0.2524:0.3429:0.4047 - - NM_000243.2,ENST00000339854,ENST00000536379 M680I,M500I,M469I 680 O15553 MEFV_HUMAN 0.79406 0.805,0.238,0.196 I 680,500,469 M G - 16 0 3 AEFGBI N 0.05886 0.01963 MEFV 0 0 15304 0 0 33578 246254 0 0 9850 0 0 17248 0 0 22296 24 2.148382e-04 111712 2 3.646973e-04 5484 0 0 30782 - - - - - - - - - - - - - - - - - - - - - - 0 0.554377 0.28343 0.000000 0.06329 0.039000 0.15576 -0.167000 0.09847 -1.090000 0.01878 3243447 C ATG neutral chr16_3293484_C/- - 2043 C - 668 G/X gGa/ga MEFV 10/10 - HET frameshift_variant - - - - - - - - - - - - - - - - - - - - - - - - - NM_000243.2:c.2003del NP_000234.1:p.Gly668GlufsTer7 chr16:3293484 4210 NM_000243.2 Transcript 2003 FMF-248 1 HIGH - -1 - deletion EntrezGene - protein_coding YES - - NP_000234.1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chr16_3297073_A/G - 1570 A G 510 D gaT/gaC MEFV 5/10 - HOM synonymous_variant benign rs224206 - - - - MEFV:D510D 5|23|23 - - - - - - - - - - - - - - - - - NM_000243.2:c.1530T>C NP_000234.1:p.Asp510= chr16:3297073 4210 NM_000243.2 Transcript 1530 FMF-248 1 LOW - -1 - SNV EntrezGene - protein_coding YES - - NP_000234.1 - - - - - - - - 0.6631 0.6936 0.6297 0.6518 0.5577 0.7658 0.6814 0.5345 0.612 0.6831 0.7395 0.5461 0.6558 0.57 0.5407 0.571 0.7283 - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chr16_3297073_A/G - 937 A G 299 D gaT/gaC MEFV 4/9 - HOM synonymous_variant benign rs224206 - - - - - - - - - - - - - - - - - - - - - - - NM_001198536.1:c.897T>C NP_001185465.1:p.Asp299= chr16:3297073 4210 NM_001198536.1 Transcript 897 FMF-248 1 LOW - -1 - SNV EntrezGene - protein_coding - - - NP_001185465.1 - - - - - - - - 0.6631 0.6936 0.6297 0.6518 0.5577 0.7658 0.6814 0.5345 0.612 0.6831 0.7395 0.5461 0.6558 0.57 0.5407 0.571 0.7283 - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chr16_3297175_T/C - 1468 T C 476 Q caA/caG MEFV 5/10 - HOM synonymous_variant benign,likely_benign rs224207 - - - - MEFV:Q476Q 6|22|24 - - - - - - - - - - - - - - - - - NM_000243.2:c.1428A>G NP_000234.1:p.Gln476= chr16:3297175 4210 NM_000243.2 Transcript 1428 FMF-248 1 LOW - -1 - SNV EntrezGene - protein_coding YES - - NP_000234.1 - - - - - - - - 0.6506 0.649 0.6239 0.6528 0.5577 0.7648 0.6395 0.5323 0.608 0.6401 0.7361 0.5456 0.6579 0.5695 0.5392 0.5678 0.7279 - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chr16_3297175_T/C - 835 T C 265 Q caA/caG MEFV 4/9 - HOM synonymous_variant benign,likely_benign rs224207 - - - - - - - - - - - - - - - - - - - - - - - NM_001198536.1:c.795A>G NP_001185465.1:p.Gln265= chr16:3297175 4210 NM_001198536.1 Transcript 795 FMF-248 1 LOW - -1 - SNV EntrezGene - protein_coding - - - NP_001185465.1 - - - - - - - - 0.6506 0.649 0.6239 0.6528 0.5577 0.7648 0.6395 0.5323 0.608 0.6401 0.7361 0.5456 0.6579 0.5695 0.5392 0.5678 0.7279 - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chr16_3297181_C/T - 1462 C T 474 E gaG/gaA MEFV 5/10 - HOM synonymous_variant benign rs224208 - - - - MEFV:E474E 4|20|25 - - - - - - - - - - - - - - - - - NM_000243.2:c.1422G>A NP_000234.1:p.Glu474= chr16:3297181 4210 NM_000243.2 Transcript 1422 FMF-248 1 LOW - -1 - SNV EntrezGene - protein_coding YES - - NP_000234.1 - - - - - - - - 0.639 0.6407 0.6239 0.6062 0.5577 0.7648 0.6331 0.5326 0.6048 0.634 0.7358 0.5456 0.6229 0.5694 0.539 0.5651 0.7275 - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chr16_3297181_C/T - 829 C T 263 E gaG/gaA MEFV 4/9 - HOM synonymous_variant benign rs224208 - - - - - - - - - - - - - - - - - - - - - - - NM_001198536.1:c.789G>A NP_001185465.1:p.Glu263= chr16:3297181 4210 NM_001198536.1 Transcript 789 FMF-248 1 LOW - -1 - SNV EntrezGene - protein_coding - - - NP_001185465.1 - - - - - - - - 0.639 0.6407 0.6239 0.6062 0.5577 0.7648 0.6331 0.5326 0.6048 0.634 0.7358 0.5456 0.6229 0.5694 0.539 0.5651 0.7275 - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chr16_3299749_G/A - 982 G A 314 R cgC/cgT MEFV 3/10 - HOM synonymous_variant benign rs224213 - - - - MEFV:R314R 7|28|29 - - - - - - - - - - - - - - - - - NM_000243.2:c.942C>T NP_000234.1:p.Arg314= chr16:3299749 4210 NM_000243.2 Transcript 942 FMF-248 1 LOW - -1 - SNV EntrezGene - protein_coding YES - - NP_000234.1 - - - - - - - - 0.6907 0.7322 0.6412 0.7083 0.5606 0.7853 0.7057 0.5394 0.6281 0.7123 0.7479 0.5728 0.7204 0.5836 0.5475 0.5843 0.7423 - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chr16_3299749_G/A - 349 G A 103 R cgC/cgT MEFV 2/9 - HOM synonymous_variant benign rs224213 - - - - - - - - - - - - - - - - - - - - - - - NM_001198536.1:c.309C>T NP_001185465.1:p.Arg103= chr16:3299749 4210 NM_001198536.1 Transcript 309 FMF-248 1 LOW - -1 - SNV EntrezGene - protein_coding - - - NP_001185465.1 - - - - - - - - 0.6907 0.7322 0.6412 0.7083 0.5606 0.7853 0.7057 0.5394 0.6281 0.7123 0.7479 0.5728 0.7204 0.5836 0.5475 0.5843 0.7423 - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chr16_3299749_G/A - 1003 G A 314 R cgC/cgT MEFV 3/5 - HOM synonymous_variant benign rs224213 - - - - MEFV:R314R 7|28|29 - - - - - - - - - - - - - - - - - XM_005255319.1:c.942C>T XP_005255376.1:p.Arg314= chr16:3299749 4210 XM_005255319.1 Transcript 942 FMF-248 1 LOW - -1 - SNV EntrezGene - protein_coding - - - XP_005255376.1 - - - - - - - - 0.6907 0.7322 0.6412 0.7083 0.5606 0.7853 0.7057 0.5394 0.6281 0.7123 0.7479 0.5728 0.7204 0.5836 0.5475 0.5843 0.7423 - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chr16_3304573_G/T - 535 G T 165 A gcC/gcA MEFV 2/10 - HET synonymous_variant benign rs224223 - - - - MEFV:A165A 3|24|30 - - - - - - - - - - - - - - - - - NM_000243.2:c.495C>A NP_000234.1:p.Ala165= chr16:3304573 4210 NM_000243.2 Transcript 495 FMF-248 1 LOW - -1 - SNV EntrezGene - protein_coding YES - - NP_000234.1 - - - - - - - - 0.3864 0.528 0.5965 0.1667 0.4732 0.183 0.4912 0.4546 0.4298 0.4963 0.6119 0.3989 0.1659 0.506 0.4745 0.4403 0.1919 - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chr16_3304573_G/T - 556 G T 165 A gcC/gcA MEFV 2/5 - HET synonymous_variant benign rs224223 - - - - MEFV:A165A 3|24|30 - - - - - - - - - - - - - - - - - XM_005255319.1:c.495C>A XP_005255376.1:p.Ala165= chr16:3304573 4210 XM_005255319.1 Transcript 495 FMF-248 1 LOW - -1 - SNV EntrezGene - protein_coding - - - XP_005255376.1 - - - - - - - - 0.3864 0.528 0.5965 0.1667 0.4732 0.183 0.4912 0.4546 0.4298 0.4963 0.6119 0.3989 0.1659 0.506 0.4745 0.4403 0.1919 - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chr16_3304654_T/C - 454 T C 138 G ggA/ggG MEFV 2/10 - HOM synonymous_variant benign rs224224 - - - - MEFV:G138G 3|28|31 - - - - - - - - - - - - - - - - - NM_000243.2:c.414A>G NP_000234.1:p.Gly138= chr16:3304654 4210 NM_000243.2 Transcript 414 FMF-248 1 LOW - -1 - SNV EntrezGene - protein_coding YES - - NP_000234.1 - - - - - - - - 0.3866 0.5257 0.5937 0.1587 0.4742 0.1963 0.4914 0.4536 0.4395 0.5049 0.6145 0.3991 0.1629 0.5154 0.4784 0.4475 0.2006 - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chr16_3304654_T/C - 475 T C 138 G ggA/ggG MEFV 2/5 - HOM synonymous_variant benign rs224224 - - - - MEFV:G138G 3|28|31 - - - - - - - - - - - - - - - - - XM_005255319.1:c.414A>G XP_005255376.1:p.Gly138= chr16:3304654 4210 XM_005255319.1 Transcript 414 FMF-248 1 LOW - -1 - SNV EntrezGene - protein_coding - - - XP_005255376.1 - - - - - - - - 0.3866 0.5257 0.5937 0.1587 0.4742 0.1963 0.4914 0.4536 0.4395 0.5049 0.6145 0.3991 0.1629 0.5154 0.4784 0.4475 0.2006 - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chr16_3304762_A/G - 346 A G 102 D gaT/gaC MEFV 2/10 - HOM synonymous_variant benign rs224225 - - - - MEFV:D102D 2|19|23 - - - - - - - - - - - - - - - - - NM_000243.2:c.306T>C NP_000234.1:p.Asp102= chr16:3304762 4210 NM_000243.2 Transcript 306 FMF-248 1 LOW - -1 - SNV EntrezGene - protein_coding YES - - NP_000234.1 - - - - - - - - 0.3894 0.5265 0.5937 0.1577 0.4732 0.2117 0.5005 0.464 0.4435 0.5068 0.6157 0.3992 0.1628 0.5156 0.4799 0.4506 0.2155 - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chr16_3304762_A/G - 367 A G 102 D gaT/gaC MEFV 2/5 - HOM synonymous_variant benign rs224225 - - - - MEFV:D102D 2|19|23 - - - - - - - - - - - - - - - - - XM_005255319.1:c.306T>C XP_005255376.1:p.Asp102= chr16:3304762 4210 XM_005255319.1 Transcript 306 FMF-248 1 LOW - -1 - SNV EntrezGene - protein_coding - - - XP_005255376.1 - - - - - - - - 0.3894 0.5265 0.5937 0.1577 0.4732 0.2117 0.5005 0.464 0.4435 0.5068 0.6157 0.3992 0.1628 0.5156 0.4799 0.4506 0.2155 - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -`

at7 commented 5 years ago

I tried my best to reproduce the missing phenotype annotations but I'm not successful. Could you please generate a much smaller version of your vep run? Could you for example only select the phenotype plugin and reduce your fields list to "Uploaded_variation,PHENOTYPES"? If this works we will at least know that there is a possible naming conflict caused by adding any of the other options. Thank you

shigej38 commented 5 years ago

edit and run the way you say. I removed the "##" character from the output for not long and formatting. (header) output is: ` ENSEMBL VARIANT EFFECT PREDICTOR v97.3 Output produced at 2019-09-05 09:05:59 Using cache in /home/detagen/.vep/homo_sapiens_refseq/97_GRCh37 Using API version 97, DB version ? ensembl-variation version 97.26a059c ensembl-funcgen version 97.24f4d3c ensembl version 97.378db18 ensembl-io version 97.dc917e1 gnomAD version r2.1 HGMD-PUBLIC version 20174 refseq version 01_2015 genebuild version 2011-04 dbSNP version 151 1000genomes version phase3 gencode version GENCODE 19 regbuild version 1.0 sift version sift5.2.2 polyphen version 2.2.2 ESP version 20141103 COSMIC version 86 assembly version GRCh37.p13 ClinVar version 201810 Column descriptions: Uploaded_variation : Identifier of uploaded variant PHENOTYPES : ?

Uploaded_variation PHENOTYPES

chr1_11854457_G/A - chr1_11854457_G/A - chr1_11854457_G/A - chr1_11854457_G/A - chr1_11854457_G/A - chr1_11854457_G/A - chr1_11854457_G/A - chr1_11854457_G/A - chr1_11854476_T/G - chr1_11854476_T/G - chr1_11854476_T/G - chr1_11854476_T/G - chr1_11854476_T/G - chr1_11854476_T/G - chr1_11854476_T/G - chr1_11854476_T/G - chr1_11856378_G/A - chr1_11856378_G/A - chr1_11856378_G/A - chr1_11856378_G/A - chr1_11856378_G/A - chr1_11856378_G/A - chr1_11856378_G/A - chr1_11856378_G/A - chr1_169519042_T/C - chr1_169519049_T/C - chr1_169519062_A/G - chr16_3293447_C/G - chr16_3293484_C/- - chr16_3297073_A/G - chr16_3297073_A/G - chr16_3297175_T/C - chr16_3297175_T/C - chr16_3297181_C/T - chr16_3297181_C/T - chr16_3299749_G/A - chr16_3299749_G/A - chr16_3299749_G/A - chr16_3304573_G/T - chr16_3304573_G/T - chr16_3304654_T/C - chr16_3304654_T/C - chr16_3304762_A/G - chr16_3304762_A/G -`

at7 commented 5 years ago

Thank you. Could you please also share the full vep command?

shigej38 commented 5 years ago

my variables is: DIR=/home/$USER/Desktop/programlar PLAYGROUND=/home/$USER/Desktop/pipeline/playground RESULT=/home/$USER/Desktop/pipeline GENOME=/home/$USER/Desktop/programlar/genome/genome.fa LOG=$RESULT/log G2PLOG=$LOG/g2plog VEP=$DIR/ensembl-vep VEPDATA=$DIR/ensembl-data CACHE=/home/$USER/.vep PHENO=$CACHE/Plugin/Phenotypes.pm_homo_sapiens_97_GRCh37.gvf.gz RESULT2=/home/$USER/Desktop/result IN=$RESULT2/input OUT=$RESULT2/output LOGDIR=$RESULT2/log MANIP=$DIR/excel-manipulation/manipulasyon.py SIRA="Uploaded_variation,PHENOTYPES

my command is: $VEP/vep --fork 1 --refseq --use_given_ref --force_overwrite --coding_only -i /home/detagen/Desktop/pipeline/playground/NECESSARY/FMF-248/FMF-248.vcf -o /home/detagen/Desktop/deneme.csv --cache --offline --assembly GRCh37 --tab --check_existing --biotype --canonical --domains --uniprot --ccds --symbol --protein --hgvs --no_escape --numbers --show_ref_allele --allele_number --individual all --regulatory --humdiv --polyphen p --sift p --variant_class --plugin dbNSFP,$VEPDATA/dbNSFP3.5/dbNSFP3.5.gz,ALL --plugin Condel,$CACHE/Plugins/config/Condel/config/condel_SP.conf,p --fasta $VEPDATA/fasta/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa --plugin Mastermind,$VEPDATA/mastermind/mastermind_cited_variants_reference-2019.06.14-grch37.vcf.gz --plugin G2P,file="$VEPDATA/G2P/DDG2P_10_7_2019.csv",log_dir="$LOGDIR/$FILE",txt_report="$LOGDIR/$FILE/$BASE.txt",html_report="$LOGDIR/$FILE/$BASE.html" --fields $SIRA --custom $VEPDATA/clinvar/clinvar_20190513.vcf.gz,ClinVar,vcf,exact,0,CLNSIG,CLNREVSTAT,CLNDN --plugin Phenotypes,file=$PHENO,include_types=Gene

at7 commented 5 years ago

I tried to replicate the same command including all the plugins you are using but I'm still not able to replicate the problem. Could you please try out the following steps and report back the results to me?

1)Could you please run with the Phenotypes plugin only: $VEP/vep --fork 1 --refseq --use_given_ref --force_overwrite --coding_only -i /home/detagen/Desktop/pipeline/playground/NECESSARY/FMF-248/FMF-248.vcf -o /home/detagen/Desktop/deneme.csv --cache --offline --assembly GRCh37 --tab --check_existing --biotype --canonical --domains --uniprot --ccds --symbol --protein --hgvs --no_escape --numbers --show_ref_allele --allele_number --individual all --regulatory --humdiv --polyphen p --sift p --variant_class --fasta $VEPDATA/fasta/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa --plugin Phenotypes,file=$PHENO,include_types=Gene

2)Could you please run with the Phenotypes plugin only and without --fields 3)Could you please run with my example vcf file small_example_phenotypes.vcf.gz 4)Could you send me your input file? But could you please send it as an attachment and not paste the content. Otherwise it will be very difficult to parse the data correctly.

Thank you! small_example_phenotypes.vcf.gz

shigej38 commented 5 years ago

with your file without --fields just with phenotype plugin used command: $VEP/vep --fork 1 --refseq --use_given_ref --force_overwrite --coding_only -i /home/detagen/Desktop/small_example_phenotypes.vcf -o /home/detagen/Desktop/small_example_phenotypes.csv --cache --offline --assembly GRCh37 --tab --check_existing --biotype --canonical --domains --uniprot --ccds --symbol --protein --hgvs --no_escape --numbers --show_ref_allele --allele_number --individual all --regulatory --humdiv --polyphen p --sift p --variant_class --fasta $VEPDATA/fasta/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa --plugin Phenotypes,file=$PHENO,include_types=Gene

output is: small_example_phenotypes.zip

and my input file (vcf) is: FMF.zip

and used command is: (with variables) $VEP/vep --fork 1 --refseq --use_given_ref --force_overwrite --coding_only -i /home/detagen/Desktop/pipeline/playground/NECESSARY/FMF-248/FMF-248.vcf -o /home/detagen/Desktop/deneme.csv --cache --offline --assembly GRCh37 --tab --check_existing --biotype --canonical --domains --uniprot --ccds --symbol --protein --hgvs --no_escape --numbers --show_ref_allele --allele_number --individual all --regulatory --humdiv --polyphen p --sift p --variant_class --fasta $VEPDATA/fasta/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa --plugin Phenotypes,file=$PHENO,include_types=Gene

is my input file output: deneme.csv.gz

at7 commented 5 years ago

Thank you very much! So when I take a look at the output file small_example_phenotypes the PHENOTYPES plugin is not mentioned in the header which makes me think that vep never runs the plugin even though you tell it to with --plugin Phenotypes,file=$PHENO,include_types=Gene From looking through your previous output I know that other plugins are run. Are you getting any error messages when you run your command? Possible errors could be --WARNING: Failed to instantiate plugin Phenotypes: ERROR: Unable to generate GFF file in offline mode --WARNING: Failed to compile plugin Phenotypes: Can't locate Phenotypes.pm Thank you

shigej38 commented 5 years ago

Yes, ı am getting one error is: --WARNING: Failed to instantiate plugin Phenotypes: ERROR: Unable to generate GFF file in offline mode

at7 commented 5 years ago

This is very helpful. Could you please check that file which you specify with $PHENO exists: --plugin Phenotypes,file=$PHENO,include_types=Gene. At the moment the plugin tries to generate the file from scratch if it cannot find the file. The plugin needs a database connection for generating the file and throws an error if vep is run in offline mode. Thank you

shigej38 commented 5 years ago

yes this file already exists

ls -l | grep Phenotypes (command runing in .vep/Plugin folder)

-rw-r--r-- 1 detagen detagen    12598 Eyl  3 17:00 Phenotypes.pm
-rw-r--r-- 1 detagen detagen 73564477 Eyl  3 17:31 Phenotypes.pm_homo_sapiens_97_GRCh37.gvf.gz
-rw-r--r-- 1 detagen detagen   599863 Eyl  3 17:31 Phenotypes.pm_homo_sapiens_97_GRCh37.gvf.gz.tbi
-rw-r--r-- 1 detagen detagen 73517770 Eyl  3 17:30 Phenotypes.pm_homo_sapiens_97_GRCh37.gvf.gz.tmp

at7 commented 5 years ago

Could you please try --plugin Phenotypes,file=/home/detagen/.vep/Plugins/Phenotypes.pm_homo_sapiens_97_GRCh37.gvf.gz,include_types=Gene Thank you!

shigej38 commented 5 years ago

Yes, the problem has been solved by specifying the file path in this way. Thank you for your patience. You are perfect.

at7 commented 5 years ago

That's great news. You probably should check what is stored in your $PHENO variable and also check where it gets possibly overwritten. I'm glad we solved the problem eventually.

shigej38 commented 5 years ago

ı am closing this is issues again thank you

Ensembl / ensembl-vep

how to write disease name from output with ensembl-vep #573

Phenotypes plugin: This will take some time but it will only run once per species, assembly and release

Phenotypes plugin: Querying database

Phenotypes plugin: Writing to file

Phenotypes plugin: Sorting file with sort

Phenotypes plugin: Indexing file with tabix

Phenotypes plugin: Generating GFF file /home/detagen/.vep/Plugins/Phenotypes.pm_homo_sapiens_97_GRCh37.gvf.gz from database

Phenotypes plugin: This will take some time but it will only run once per species, assembly and release

Phenotypes plugin: Querying database

Phenotypes plugin: Writing to file

Phenotypes plugin: Sorting file with sort

Phenotypes plugin: Indexing file with tabix

Uploaded_variation PHENOTYPES