ClinVar Miner

Submissions for variant NM_000545.8(HNF1A):c.1295C>G (p.Ser432Cys)

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Total submissions: 1
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ClinGen Monogenic Diabetes Variant Curation Expert Panel RCV003318532 SCV004022356 uncertain significance Monogenic diabetes 2023-07-30 reviewed by expert panel curation The c.1295C>G variant in the HNF1 homeobox A gene, HNF1A, causes an amino acid change of serine to cysteine at codon 432 (p.(Ser432Cys)) of NM_000545.8. This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.8949, which is greater than the MDEP VCEP threshold of 0.70 (PP3). This variant has an incomputable Popmax filtering allele frequency due to 0 copies in the European non-Finnish and 1 copy in another subpopulation (East Asian), which is less than the ClinGen MDEP threshold for PM2_Supporting (ENF Popmax FAF < 0.000003 and <=2 copies in ENF and <= 1 copy in any other subpopulation) (PM2_Supporting). Two other missense variants, c.1295C>T p.Ser432Phe and c.1295C>A p.Ser432Tyr, have been classified as VUS by the ClinGen MDEP; therefore, PM5 will not be applied. This variant was identified in an individual with a diabetes; however, PP4 is unable to be evaluated due to insufficient clinical information (PMID: 10588527). In summary, c.1295C>G meets the criteria to be classified as a variant of uncertain significance for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP (specification version 2.0.0, approved 1/11/2023): PP3, PM2_Supporting.

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