Open zshuyinggg opened 1 year ago
Here is the xml information for another variant:
<ClinVarSet ID="92170778"> <RecordStatus>current</RecordStatus> <Title>NM_000162.5(GCK):c.483G>A (p.Lys161=) AND Maturity-onset diabetes of the young type 2</Title> <ReferenceClinVarAssertion ID="87390" DateLastUpdated="2022-04-23" DateCreated="2013-04-04"> <ClinVarAccession Acc="RCV000029887" DateUpdated="2022-04-23" DateCreated="2013-04-04" Version="2" Type="RCV"/> <RecordStatus>current</RecordStatus> <ClinicalSignificance DateLastEvaluated="2011-08-18"> <ReviewStatus>criteria provided, single submitter</ReviewStatus> <Description>Likely pathogenic</Description> </ClinicalSignificance> <Assertion Type="variation to disease"/> <AttributeSet> <Attribute Type="ModeOfInheritance" integerValue="262">Autosomal dominant inheritance</Attribute> </AttributeSet> <ObservedIn> <Sample> <Origin>germline</Origin> <Species TaxonomyId="9606">human</Species> <AffectedStatus>unknown</AffectedStatus> </Sample> <Method> <Purpose>assert pathogenicity</Purpose> <MethodType>clinical testing</MethodType> </Method> <ObservedData ID="95519857"> <Attribute integerValue="3" Type="VariantAlleles"/> </ObservedData> </ObservedIn> <ObservedIn> <Sample> <Origin>germline</Origin> <Species TaxonomyId="9606">human</Species> <AffectedStatus>yes</AffectedStatus> <NumberTested>3</NumberTested> </Sample> <Method> <MethodType>curation</MethodType> </Method> <ObservedData ID="96289752"> <Attribute integerValue="3" Type="VariantAlleles"/> </ObservedData> </ObservedIn> <MeasureSet Type="Variant" ID="36224" Acc="VCV000036224" Version="2"> <Measure Type="single nucleotide variant" ID="44888"> <Name> <ElementValue Type="Preferred">NM_000162.5(GCK):c.483G>A (p.Lys161=)</ElementValue> </Name> <CanonicalSPDI>NC_000007.14:44150955:C:T</CanonicalSPDI> <AttributeSet> <Attribute Accession="LRG_1074t1" Type="HGVS, coding, LRG">LRG_1074t1:c.483G>A</Attribute> </AttributeSet> <AttributeSet> <Attribute Accession="LRG_1074t2" Type="HGVS, coding, LRG">LRG_1074t2:c.486G>A</Attribute> </AttributeSet> <AttributeSet> <Attribute Accession="NM_033508" Version="3" Change="c.480G>A" Type="HGVS, coding, RefSeq">NM_033508.3:c.480G>A</Attribute> </AttributeSet> <AttributeSet> <Attribute Accession="NM_000162" Version="5" Change="c.483G>A" Type="HGVS, coding, RefSeq" MANESelect="true">NM_000162.5:c.483G>A</Attribute> </AttributeSet> <AttributeSet> <Attribute Accession="NM_001354800" Version="1" Change="c.483G>A" Type="HGVS, coding, RefSeq">NM_001354800.1:c.483G>A</Attribute> </AttributeSet> <AttributeSet> <Attribute Accession="NM_033507" Version="3" Change="c.486G>A" Type="HGVS, coding, RefSeq">NM_033507.3:c.486G>A</Attribute> </AttributeSet> <AttributeSet> <Attribute Accession="LRG_1074" Type="HGVS, genomic, LRG">LRG_1074:g.52215G>A</Attribute> </AttributeSet> <AttributeSet> <Attribute Accession="NG_008847" Version="2" Change="g.52215G>A" Type="HGVS, genomic, RefSeqGene">NG_008847.2:g.52215G>A</Attribute> </AttributeSet> <AttributeSet> <Attribute Accession="NC_000007" Version="14" Change="g.44150956C>T" Type="HGVS, genomic, top level" integerValue="38">NC_000007.14:g.44150956C>T</Attribute> </AttributeSet> <AttributeSet> <Attribute Accession="NC_000007" Version="13" Change="g.44190555C>T" Type="HGVS, genomic, top level, previous" integerValue="37">NC_000007.13:g.44190555C>T</Attribute> </AttributeSet> <AttributeSet> <Attribute Accession="NM_000162" Version="3" Change="c.483G>A" Type="HGVS, previous">NM_000162.3:c.483G>A</Attribute> </AttributeSet> <AttributeSet> <Attribute Type="HGVS, protein"/> </AttributeSet> <AttributeSet> <Attribute Accession="LRG_1074p1" Change="p.Lys161=" Type="HGVS, protein">LRG_1074p1:p.Lys161=</Attribute> </AttributeSet> <AttributeSet> <Attribute Accession="LRG_1074p2" Change="p.Lys162=" Type="HGVS, protein">LRG_1074p2:p.Lys162=</Attribute> </AttributeSet> <AttributeSet> <Attribute Accession="NP_277043" Version="1" Change="p.Lys160=" Type="HGVS, protein, RefSeq">NP_277043.1:p.Lys160=</Attribute> </AttributeSet> <AttributeSet> <Attribute Accession="NP_000153" Version="1" Change="p.Lys161=" Type="HGVS, protein, RefSeq">NP_000153.1:p.Lys161=</Attribute> </AttributeSet> <AttributeSet> <Attribute Accession="NP_001341729" Version="1" Change="p.Lys161=" Type="HGVS, protein, RefSeq">NP_001341729.1:p.Lys161=</Attribute> </AttributeSet> <AttributeSet> <Attribute Accession="NP_277042" Version="1" Change="p.Lys162=" Type="HGVS, protein, RefSeq">NP_277042.1:p.Lys162=</Attribute> </AttributeSet> <AttributeSet> <Attribute Type="MolecularConsequence">synonymous variant</Attribute> <XRef ID="SO:0001819" DB="Sequence Ontology"/> <XRef ID="NM_000162.5:c.483G>A" DB="RefSeq"/> </AttributeSet> <AttributeSet> <Attribute Type="MolecularConsequence">synonymous variant</Attribute> <XRef ID="SO:0001819" DB="Sequence Ontology"/> <XRef ID="NM_001354800.1:c.483G>A" DB="RefSeq"/> </AttributeSet> <AttributeSet> <Attribute Type="MolecularConsequence">synonymous variant</Attribute> <XRef ID="SO:0001819" DB="Sequence Ontology"/> <XRef ID="NM_033507.3:c.486G>A" DB="RefSeq"/> </AttributeSet> <AttributeSet> <Attribute Type="MolecularConsequence">synonymous variant</Attribute> <XRef ID="SO:0001819" DB="Sequence Ontology"/> <XRef ID="NM_033508.3:c.480G>A" DB="RefSeq"/> </AttributeSet> <CytogeneticLocation>7p13</CytogeneticLocation> <SequenceLocation Assembly="GRCh38" AssemblyAccessionVersion="GCF_000001405.38" AssemblyStatus="current" Chr="7" Accession="NC_000007.14" start="44150956" stop="44150956" display_start="44150956" display_stop="44150956" variantLength="1" positionVCF="44150956" referenceAlleleVCF="C" alternateAlleleVCF="T"/> <SequenceLocation Assembly="GRCh37" AssemblyAccessionVersion="GCF_000001405.25" AssemblyStatus="previous" Chr="7" Accession="NC_000007.13" start="44190555" stop="44190555" display_start="44190555" display_stop="44190555" variantLength="1" positionVCF="44190555" referenceAlleleVCF="C" alternateAlleleVCF="T"/> <MeasureRelationship Type="within single gene"> <Name> <ElementValue Type="Preferred">glucokinase</ElementValue> </Name> <Symbol> <ElementValue Type="Preferred">GCK</ElementValue> </Symbol> <SequenceLocation Assembly="GRCh38" AssemblyAccessionVersion="GCF_000001405.38" AssemblyStatus="current" Chr="7" Accession="NC_000007.14" start="44143213" stop="44189439" display_start="44143213" display_stop="44189439" Strand="-"/> <SequenceLocation Assembly="GRCh37" AssemblyAccessionVersion="GCF_000001405.25" AssemblyStatus="previous" Chr="7" Accession="NC_000007.13" start="44183869" stop="44229021" display_start="44183869" display_stop="44229021" variantLength="45153" Strand="-"/> <XRef ID="2645" DB="Gene"/> <XRef Type="MIM" ID="138079" DB="OMIM"/> <XRef ID="HGNC:4195" DB="HGNC"/> </MeasureRelationship> <XRef Type="rs" ID="193922302" DB="dbSNP"/> </Measure> <Name> <ElementValue Type="Preferred">NM_000162.5(GCK):c.483G>A (p.Lys161=)</ElementValue> </Name> <XRef ID="CA213792" DB="ClinGen"/> </MeasureSet> <TraitSet Type="Disease" ID="6270"> <Trait ID="5458" Type="Disease"> <Name> <ElementValue Type="Preferred">Maturity-onset diabetes of the young type 2</ElementValue> <XRef ID="MONDO:0007453" DB="MONDO"/> </Name> <Name> <ElementValue Type="Alternate">MODY type 2</ElementValue> </Name> <Name> <ElementValue Type="Alternate">Diabetes mellitus MODY type 2</ElementValue> </Name> <Name> <ElementValue Type="Alternate">MODY glucokinase-related</ElementValue> </Name> <Name> <ElementValue Type="Alternate">Diabetes mellitus, type II, autosomal dominant</ElementValue> </Name> <Symbol> <ElementValue Type="Alternate">MODY2</ElementValue> <XRef Type="MIM" ID="125851" DB="OMIM"/> </Symbol> <AttributeSet> <Attribute Type="disease mechanism" integerValue="273">loss of function</Attribute> <XRef ID="GTR000512295" DB="Genetic Testing Registry (GTR)"/> <XRef ID="GTR000512817" DB="Genetic Testing Registry (GTR)"/> <XRef ID="GTR000552325" DB="Genetic Testing Registry (GTR)"/> <XRef ID="GTR000552542" DB="Genetic Testing Registry (GTR)"/> <XRef ID="GTR000552544" DB="Genetic Testing Registry (GTR)"/> <XRef ID="GTR000556820" DB="Genetic Testing Registry (GTR)"/> <XRef ID="GTR000556824" DB="Genetic Testing Registry (GTR)"/> <XRef ID="GTR000557910" DB="Genetic Testing Registry (GTR)"/> <XRef ID="GTR000558434" DB="Genetic Testing Registry (GTR)"/> <XRef ID="GTR000559250" DB="Genetic Testing Registry (GTR)"/> <XRef ID="GTR000568234" DB="Genetic Testing Registry (GTR)"/> <XRef ID="GTR000570044" DB="Genetic Testing Registry (GTR)"/> <XRef ID="GTR000595971" DB="Genetic Testing Registry (GTR)"/> </AttributeSet> <AttributeSet> <Attribute Type="GARD id" integerValue="10657"/> <XRef ID="10657" DB="Office of Rare Diseases"/> </AttributeSet> <Citation Type="review" Abbrev="GeneReviews"> <ID Source="PubMed">29792621</ID> <ID Source="BookShelf">NBK500456</ID> </Citation> <XRef ID="MONDO:0007453" DB="MONDO"/> <XRef ID="C0342277" DB="MedGen"/> <XRef ID="552" DB="Orphanet"/> <XRef Type="MIM" ID="125851" DB="OMIM"/> </Trait> </TraitSet> </ReferenceClinVarAssertion> <ClinVarAssertion ID="56692"> <ClinVarSubmissionID localKey="GCK_483G_A_112110" submitter="Women's Health and Genetics/Laboratory Corporation of America, LabCorp" title="GCK:c.483G>A and MODY2"/> <ClinVarAccession Acc="SCV000052542" DateCreated="2013-04-04" DateUpdated="2022-04-07" Version="2" Type="SCV" OrgID="500026" OrganizationCategory="laboratory" OrgType="primary"/> <RecordStatus>current</RecordStatus> <ClinicalSignificance DateLastEvaluated="2011-08-18"> <ReviewStatus>criteria provided, single submitter</ReviewStatus> <Description>likely pathogenic</Description> <Citation Type="general"> <ID Source="PubMed">19564454</ID> </Citation> <Comment>Converted during submission to Likely pathogenic.</Comment> </ClinicalSignificance> <Assertion Type="variation to disease"/> <AttributeSet> <Attribute Type="ModeOfInheritance">autosomal dominant</Attribute> </AttributeSet> <AttributeSet> <Attribute Type="AssertionMethod">LabCorp Variant Classification Summary - May 2015</Attribute> <Citation Type="general"> <URL>https://submit.ncbi.nlm.nih.gov/ft/byid/rtxspsnt/labcorp_variant_classification_method_-_may_2015.pdf</URL> </Citation> </AttributeSet> <ObservedIn> <Sample> <Origin>germline</Origin> <Species TaxonomyId="9606">human</Species> <AffectedStatus>yes</AffectedStatus> <NumberTested>3</NumberTested> </Sample> <Method> <MethodType>curation</MethodType> </Method> <ObservedData> <Attribute Type="VariantAlleles" integerValue="3"/> <Citation Type="general"> <ID Source="PubMed">19564454</ID> </Citation> <Comment>Author mentions it to be novel mutation and is said to be found along three consecutive generations of affected family members, So assumed atleast three individuals from the family carrying this mutation, Even it is silent mutation, author considered it as pathogenic variant as G>A, as the variation opccured at the last exonic nucleotide of exon 4 disrupting the highly conserved exonic consensus sequence of splice site. Not seen in Controls see PbGP.</Comment> </ObservedData> </ObservedIn> <ObservedIn> <Sample> <Origin>germline</Origin> <Tissue>Blood</Tissue> <Species TaxonomyId="9606">human</Species> <AffectedStatus>unknown</AffectedStatus> </Sample> <Method> <Purpose>assert pathogenicity</Purpose> <MethodType>clinical testing</MethodType> </Method> <ObservedData> <Attribute Type="VariantAlleles">1</Attribute> </ObservedData> <Co-occurrenceSet> <Zygosity>SingleHeterozygote</Zygosity> <AlleleDescSet> <Name>GCK:c.645C>T</Name> <Zygosity>SingleHeterozygote</Zygosity> </AlleleDescSet> <AlleleDescSet> <Name>GCK:c.1019+18G>A</Name> <Zygosity>SingleHeterozygote</Zygosity> </AlleleDescSet> <AlleleDescSet> <Name>TCF1:c.79A>C</Name> <Zygosity>SingleHeterozygote</Zygosity> </AlleleDescSet> <AlleleDescSet> <Name>TCF1:c.51C>G</Name> <Zygosity>SingleHeterozygote</Zygosity> </AlleleDescSet> <AlleleDescSet> <Name>TCF1:c.1501+7G>A</Name> <Zygosity>SingleHeterozygote</Zygosity> </AlleleDescSet> <AlleleDescSet> <Name>TCF1:c.1460G>A</Name> <Zygosity>SingleHeterozygote</Zygosity> </AlleleDescSet> <AlleleDescSet> <Name>TCF1:c.1375C>T</Name> <Zygosity>SingleHeterozygote</Zygosity> </AlleleDescSet> <AlleleDescSet> <Name>TCF1:c.1720A>G</Name> <Zygosity>Homozygote</Zygosity> </AlleleDescSet> <Count>1</Count> </Co-occurrenceSet> </ObservedIn> <ObservedIn> <Sample> <Origin>germline</Origin> <Tissue>Blood</Tissue> <Species TaxonomyId="9606">human</Species> <AffectedStatus>unknown</AffectedStatus> </Sample> <Method> <Purpose>assert pathogenicity</Purpose> <MethodType>clinical testing</MethodType> </Method> <ObservedData> <Attribute Type="VariantAlleles">1</Attribute> </ObservedData> <Co-occurrenceSet> <Zygosity>SingleHeterozygote</Zygosity> <AlleleDescSet> <Name>GCK:c.645C>T</Name> <Zygosity>SingleHeterozygote</Zygosity> </AlleleDescSet> <AlleleDescSet> <Name>TCF1:c.864G>C</Name> <Zygosity>SingleHeterozygote</Zygosity> </AlleleDescSet> <AlleleDescSet> <Name>TCF1:c.79A>C</Name> <Zygosity>SingleHeterozygote</Zygosity> </AlleleDescSet> <AlleleDescSet> <Name>TCF1:c.51C>G</Name> <Zygosity>SingleHeterozygote</Zygosity> </AlleleDescSet> <AlleleDescSet> <Name>TCF1:c.1545G>A</Name> <Zygosity>SingleHeterozygote</Zygosity> </AlleleDescSet> <AlleleDescSet> <Name>TCF1:c.1501+7G>A</Name> <Zygosity>SingleHeterozygote</Zygosity> </AlleleDescSet> <AlleleDescSet> <Name>TCF1:c.1460G>A</Name> <Zygosity>SingleHeterozygote</Zygosity> </AlleleDescSet> <AlleleDescSet> <Name>TCF1:c.1375C>T</Name> <Zygosity>SingleHeterozygote</Zygosity> </AlleleDescSet> <AlleleDescSet> <Name>TCF1:c.1720A>G</Name> <Zygosity>Homozygote</Zygosity> </AlleleDescSet> <Count>1</Count> </Co-occurrenceSet> </ObservedIn> <ObservedIn> <Sample> <Origin>germline</Origin> <Tissue>Blood</Tissue> <Species TaxonomyId="9606">human</Species> <AffectedStatus>unknown</AffectedStatus> </Sample> <Method> <Purpose>assert pathogenicity</Purpose> <MethodType>clinical testing</MethodType> </Method> <ObservedData> <Attribute Type="VariantAlleles">1</Attribute> </ObservedData> <Co-occurrenceSet> <Zygosity>SingleHeterozygote</Zygosity> <AlleleDescSet> <Name>GCK:c.645C>T</Name> <Zygosity>SingleHeterozygote</Zygosity> </AlleleDescSet> <AlleleDescSet> <Name>GCK:c.1253+8C>T</Name> <Zygosity>SingleHeterozygote</Zygosity> </AlleleDescSet> <Count>1</Count> </Co-occurrenceSet> </ObservedIn> <MeasureSet Type="Variant"> <Measure Type="single nucleotide variant"> <AttributeSet> <Attribute Type="HGVS">NM_000162.3:c.483G>A</Attribute> </AttributeSet> <AttributeSet> <Attribute Type="HGVS">p.Lys161Lys</Attribute> </AttributeSet> <AttributeSet> <Attribute Type="MolecularConsequence">synonymous mutation</Attribute> <XRef DB="Sequence Ontology" ID="SO:0001588"/> </AttributeSet> <MeasureRelationship Type="variant in gene"> <Symbol> <ElementValue Type="Preferred">GCK</ElementValue> </Symbol> </MeasureRelationship> </Measure> </MeasureSet> <TraitSet Type="Disease"> <Trait Type="Disease"> <Name> <ElementValue Type="Preferred">MODY2</ElementValue> </Name> <Symbol> <ElementValue Type="Preferred">MODY2</ElementValue> </Symbol> </Trait> </TraitSet> </ClinVarAssertion> </ClinVarSet>
We have hgvs information for this variant, but it does not provide uniprot ID.
Here is the xml information for another variant:
We have hgvs information for this variant, but it does not provide uniprot ID.
Question: