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Clarify immunodeficiencies involving POLD1 and POLD2 #8082

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cmungall opened this issue Aug 21, 2024 · 2 comments
Open

Clarify immunodeficiencies involving POLD1 and POLD2 #8082

cmungall opened this issue Aug 21, 2024 · 2 comments
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@cmungall
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cmungall commented Aug 21, 2024

We have a term that was added in #5261

id: MONDO:0800145
name: non-severe combined immunodeficiency due to polymerase delta deficiency
def: "Any non-severe combined immunodeficiency in which the cause of the disease is variation in the POLD1/POLD2 gene." [PMID:31449058]
subset: clingen {source="MONDO:CLINGEN"}
subset: gard_rare {source="MONDO:GARD"}
subset: rare
is_a: MONDO:0018814 {source="https://orcid.org/0000-0002-7371-8158", source="https://orcid.org/0000-0003-0113-912X"} ! non-SCID combined immunodeficiency
relationship: curated_content_resource https://search.clinicalgenome.org/kb/conditions/MONDO:0800145 {source="MONDO:CLINGEN"}
relationship: RO:0002573 HP:0000007 {source="https://orcid.org/0000-0002-7371-8158", source="https://orcid.org/0000-0003-0113-912X"} ! has modifier Autosomal recessive inheritance
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/5261" xsd:anyURI

This doesn't conform to a DP. We don't have a DP for disjunctions of genes.

It's important to conform to DPs because otherwise the ontology becomes too hard to manage. For example, we also have:

id: MONDO:0970994
name: immunodeficiency 120
xref: OMIM:620836 {source="MONDO:equivalentTo"}
is_a: MONDO:0021094 {source="OMIM:620836", source="https://orcid.org/0000-0002-4142-7153"} ! immunodeficiency disease

This is caused by POLD1 (why don't we have the edge linking to gene?)

What is the relationship between these two MONDO IDs? Right now they are unlinked, but they are clearly part of the same spectrum of deficiencies involving one or more parts of the POLD complex.

@cmungall
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Note that OMIM annotated the same paper and collected in under https://omim.org/entry/620836 (immunodeficiency 120)

@aslgraefe
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USIDNET2024 for POLD1 & POLD2:
Inheritance: AR
Associated Features: Recurrent respiratory tract infections, skin infections, warts and molluscum, short stature, intellectual disability; T cell count: Low Low CD4 T cells; low B cell count; low Immunoglobulin levels

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