The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
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Variant: NM_175914.5(HNF4A):c.925C>T (p.Arg309Cys)

CA207744

36364 (ClinVar)

Gene: HNF4A
Condition: monogenic diabetes
Inheritance Mode: Autosomal dominant inheritance
UUID: 09205e51-4a3a-4e2d-a6a3-bb1f8159b636
Approved on: 2024-04-06
Published on: 2024-04-06

HGVS expressions

NM_175914.5:c.925C>T
NM_175914.5(HNF4A):c.925C>T (p.Arg309Cys)
NC_000020.11:g.44424116C>T
CM000682.2:g.44424116C>T
NC_000020.10:g.43052756C>T
CM000682.1:g.43052756C>T
NC_000020.9:g.42486170C>T
NG_009818.1:g.73316C>T
ENST00000316673.9:c.925C>T
ENST00000316099.10:c.991C>T
ENST00000619550.5:c.965C>T
ENST00000316099.9:c.991C>T
ENST00000316099.8:c.991C>T
ENST00000316673.8:c.925C>T
ENST00000372920.1:c.*758C>T
ENST00000415691.2:c.991C>T
ENST00000443598.6:c.991C>T
ENST00000457232.5:c.925C>T
ENST00000609795.5:c.925C>T
ENST00000619550.4:c.916C>T
NM_000457.4:c.991C>T
NM_001030003.2:c.925C>T
NM_001030004.2:c.925C>T
NM_001258355.1:c.970C>T
NM_001287182.1:c.916C>T
NM_001287183.1:c.916C>T
NM_001287184.1:c.916C>T
NM_175914.4:c.925C>T
NM_178849.2:c.991C>T
NM_178850.2:c.991C>T
NM_001030003.3:c.925C>T
NM_001030004.3:c.925C>T
NM_001258355.2:c.970C>T
NM_001287182.2:c.916C>T
NM_001287184.2:c.916C>T
NM_178849.3:c.991C>T
NM_178850.3:c.991C>T
NM_000457.5:c.991C>T
NM_000457.6:c.991C>T
NM_001287183.2:c.916C>T
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Pathogenic

Met criteria codes 6
PP4_Moderate PS4 PP3 PP1_Moderate PM2_Supporting PM1_Supporting

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Monogenic Diabetes Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for HNF4A Version 2.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.925C>T variant in the Hepatocyte Nuclear Factor 4 Alpha gene, HNF4A, causes an amino acid change of Arginine to Cysteine at codon 309 (p.(Arg309Cys)) of NM_175914.5. This variant was identified in at least 10 unrelated individuals with non-autoimmune and non-absolute/near-absolute insulin-deficient diabetes (PS4; Internal lab contributors). This variant is located within the ligand-binding domain of HNF4A, which is defined as critical for the protein’s function by the ClinGen MDEP (PM1_Supporting). This variant has a gnomAD v2.1.1 Grpmax filtering allele frequency of 0.000002970 (below the MDEP threshold of 0.000003) and ≤ 2 copies observed in the European non-Finnish population and ≤ 1 copy in any other subpopulation, thereby meeting the ClinGen MDEP criteria for PM2_Supporting (PM2_Supporting). This variant segregated with diabetes, with 1 informative meiosis in each of 3 families with MODY (PP1_moderate; Internal lab contributors). This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.787, which is greater than to the MDEP VCEP threshold of 0.70 (PP3). This variant was identified in several individuals with a clinical history highly specific for HNF4A-MODY (MODY probability calculator result >50%, negative genetic testing for HNF1A, responsiveness to sulfonylureas, and 1 family member with persistent neonatal hypoglycemia) (PP4_Moderate; Internal lab contributors). In summary, c.925C>T meets the criteria to be classified as Pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP (specification version 2.0.0, approved 10/11/2023): PS4, PM1_Supporting, PM2_Supporting, PP1_Moderate, PP3, PP4_Moderate.
Met criteria codes
PP4_Moderate
This variant was identified in several individuals with a clinical history highly specific for HNF4A-MODY (MODY probability calculator result >50%, negative genetic testing for HNF1A, responsiveness to sulfonylureas, and 1 family member with persistent neonatal hypoglycemia) (PP4_Moderate; Internal lab contributors).
PS4
This variant was identified in at least 10 unrelated individuals with non- autoimmune and non-absolute/near-absolute insulin-deficient diabetes (PS4; Internal lab contributors).
PP3
REVEL 0.787
PP1_Moderate
This variant segregated with diabetes, with 1 informative meiosis in each of 3 families with MODY (PP1_Moderate; Internal lab contributors).
PM2_Supporting
This variant has a gnomAD v2.1.1 Grpmax filtering allele frequency of 0.000002970 (below the MDEP threshold of 0.000003) and ≤ 2 copies observed in the European non-Finnish population and ≤ 1 copy in any other subpopulation, thereby meeting the ClinGen MDEP criteria for PM2_Supporting (PM2_Supporting).
PM1_Supporting
This variant is located within the ligand-binding domain of HNF4A, which is defined as critical for the protein’s function by the ClinGen MDEP (PM1_Supporting).
Curation History
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