Review leukoencephalopathy with vanishing white matter/CACH branch

[kanems]

OMIM has recently created an entry that uses "Cree Leukoencephalopathy" as an alternate name (https://www.omim.org/entry/620315), but this is used as a preferred name on MONDO:0020507 (we have to have unique names for submissions to ClinVar or GTR, which is how I found this particular case)

It looks like, perhaps, ORPHA:99854 is equivalent to OMIM PS603896 (based on all 5 EIF2B subunits mapping to both terms). https://www.orpha.net/consor/cgi-bin/OC_Exp.php?Lng=EN&Expert=99854 & https://omim.org/phenotypicSeries/PS603896 Also OMIM 603896 has been renamed ("Leukoencephalopathy with vanishing white matter 1, with or without ovarian failure") so the OMIM x-ref on MONDO:0011380 should also be updated.

[nicolevasilevsky]

@ahamosh is CACH syndrome in Orphanet equivalent to the OMIMPS for Leukoencephalopathy with vanishing white matter?

[nicolevasilevsky]

Note to self, these are the 5 subtypes of Leukoencephalopathy with vanishing white matter. These have not been added to Mondo yet.

• OMIM:620313 Leukoencephalopathy with vanishing white matter 3, with or without ovarian failure
• OMIM:620314 Leukoencephalopathy with vanishing white matter 4, with or without ovarian failure
• OMIM:620315 Leukoencephalopathy with vanishing white matter 5, with or without ovarian failure
• OMIM:603896Leukoencephalopathy with vanishing white matter 1, with or without ovarian failure
• OMIM:620312 Leukoencephalopathy with vanishing white matter 2, with or without ovarian failure

[ahamosh]

@nicolevasilevsky yes, CACH syndrome is the same as OMIM PS603896. And Cree Leukoencephalopathy has been renamed to live in this series.

[nicolevasilevsky]

perfect, thanks @ahamosh!

[nicolevasilevsky]

To do: need to split MONDO:0011380 'leukoencephalopathy with vanishing white matter' into

• [x] create new term [Term] id: MONDO:0800439 name: leukoencephalopathy with vanishing white matter def: "A new leukoencephalopathy, the CACH syndrome (Childhood Ataxia with Central nervous system Hypomyelination) or VWM (Vanishing White Matter) was identified on clinical and MRI criteria. Classically, this disease is characterized by (1) an onset between 2 and 5 years of age, with a cerebello-spastic syndrome exacerbated by episodes of fever or head trauma leading to death after 5 to 10 years of disease evolution, (2) a diffuse involvement of the white matter on cerebral MRI with a CSF-like signal intensity (cavitation), (3) a recessive autosomal mode of inheritance, (4) neuropathologic findings consistent with a cavitating orthochromatic leukodystrophy with increased number of oligodendrocytes with sometimes ``foamy'' aspect." [Orphanet:135] subset: ordo_disease {source="Orphanet:135"} synonym: "CACH" EXACT ABBREVIATION [DOID:0060868] synonym: "CACH syndrome" RELATED [Orphanet:135] synonym: "CACH/VWM" RELATED [GARD:0000231] synonym: "CACH/VWM syndrome" RELATED [GARD:0000231] synonym: "childhood ataxia with central nervous system hypomyelination" EXACT [DOID:0060868] synonym: "childhood ataxia with central nervous system hypomyelination/vanishing white matter" RELATED [GARD:0000231] synonym: "childhood ataxia with central nervous system hypomyelinization" RELATED [OMIM:603896] synonym: "childhood ataxia with diffuse central nervous system hypomyelination" EXACT [Orphanet:135] synonym: "CLE" RELATED EXCLUDE [DOID:0060868] synonym: "Cree leukoencehalopathy" RELATED [GARD:0000231] synonym: "Cree leukoencephalopathy" NARROW [DOID:0060868, OMIM:603896] synonym: "leukoencephalopathy with vanishing WHITE matter" RELATED [OMIM:603896] synonym: "leukoencephalopathy with vanishing white matter" EXACT CLINGEN_PREFERRED [MONDO:Lexical, OMIM:603896, Orphanet:135] synonym: "myelinosis centralis diffusa" EXACT [Orphanet:135] synonym: "ovarioleukodystrophy" RELATED [OMIM:603896] synonym: "vanishing white matter disease" RELATED [GARD:0000231] synonym: "vanishing White matter leukodystrophy" RELATED [OMIM:603896] synonym: "vanishing white matter leukodystrophy" EXACT [DOID:0060868] synonym: "vanishing White matter leukodystrophy with ovarian failure" RELATED [OMIM:603896] synonym: "VWM" RELATED ABBREVIATION [MONDO:Lexical, OMIM:603896] xref: DOID:0060868 {source="MONDO:equivalentTo"} xref: GARD:0000231 {source="MONDO:equivalentTo"} xref: ICD10CM:E75.2 {source="Orphanet:135/attributed", source="Orphanet:135/ntbt", source="DOID:0060868", source="Orphanet:135"} xref: MESH:C537420 {source="Orphanet:135/e", source="Orphanet:135"} xref: NCIT:C122664 {source="MONDO:equivalentTo"} xref: OMIMPS:603896 {source="MONDO:equivalentTo"} xref: Orphanet:135 {source="OMIM:603896", source="MONDO:equivalentTo", source="DOID:0060868"} xref: SCTID:447351004 {source="MONDO:equivalentTo"} xref: UMLS:C1847967 {source="OMIM:603896"} xref: UMLS:C1858991 {source="OMIM:603896", source="Orphanet:135/e", source="MONDO:equivalentTo", source="MONDO:ncbi_mim2gene_medline", source="NCIT:C122664", source="Orphanet:135"} xref: UMLS:C2931489 {source="Orphanet:135/e", source="MONDO:notFoundInDiseaseSubset", source="Orphanet:135"} xref: UMLS:CN199219 {source="MONDO:equivalentTo"} is_a: MONDO:0019046 {source="DOID:0060868", source="Orphanet:135"} ! leukodystrophy property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6216" xsd:anyURI

• [x] move xref: OMIM:603896 {source="MONDO:equivalentTo"} to id: MONDO:0020507

• [x] rename to leukoencephalopathy with vanishing white matter 1

• [x] add def: "Any leukoencephalopathy with vanishing white matter in which the cause of the disease is a variation in the EIF2B1 gene." [MONDO:patterns/disease_series_by_gene]

• [x] add source: is_a: MONDO:0011380 {source="OMIM:603896"} ! leukoencephalopathy with vanishing white matter

• [x] merge MONDO:0011380 'leukoencephalopathy with vanishing white matter' with MONDO:0800439 leukoencephalopathy with vanishing white matter sh run.sh owltools --use-catalog mondo-edit.obo --obsolete-replace MONDO:0011380 MONDO:0800448 -o -f obo mondo-edit.obo

[nicolevasilevsky]

I emailed David at Orphanet on 2023-06-21 (subject: Question about CACH syndrome ORPHA:135):

[nicolevasilevsky]

@sabrinatoro FYI - there is one outstanding mapping for OMIM (https://github.com/monarch-initiative/mondo-ingest/blob/main/src/ontology/lexmatch/unmapped_omim_lex.tsv) but I am unclear OMIM:620315 leukoencephalopathy with vanishing white matter 5 should be mapped to MONDO:0020507 Cree leukoencephalopathy or if it should be it's own term. Hopefully I can get some clarification from Orphanet before proceeding.

[nicolevasilevsky]

We haven't heard back from Orphanet, I sent them another message on 2023-08-22.

[ahamosh]

VWM5 and Cree Leukoencephalopathy are the same condition. The mappings are out of date and incorrect in Orphanet.

[nicolevasilevsky]

Thanks @ahamosh!