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
  • No CSPEC computer assertion could be determined for this classification!


Variant: NM_175914.5(HNF4A):c.926G>A (p.Arg309His)

CA9870414

424599 (ClinVar)

Gene: HNF4A
Condition: monogenic diabetes
Inheritance Mode: Autosomal dominant inheritance
UUID: b1c3d8a7-0981-4a14-a3aa-a9fe0f2b0d5b
Approved on: 2024-08-01
Published on: 2024-08-02

HGVS expressions

NM_175914.5:c.926G>A
NM_175914.5(HNF4A):c.926G>A (p.Arg309His)
NC_000020.11:g.44424117G>A
CM000682.2:g.44424117G>A
NC_000020.10:g.43052757G>A
CM000682.1:g.43052757G>A
NC_000020.9:g.42486171G>A
NG_009818.1:g.73317G>A
ENST00000316673.9:c.926G>A
ENST00000316099.10:c.992G>A
ENST00000619550.5:c.966G>A
ENST00000316099.9:c.992G>A
ENST00000316099.8:c.992G>A
ENST00000316673.8:c.926G>A
ENST00000372920.1:c.*759G>A
ENST00000415691.2:c.992G>A
ENST00000443598.6:c.992G>A
ENST00000457232.5:c.926G>A
ENST00000609795.5:c.926G>A
ENST00000619550.4:c.917G>A
NM_000457.4:c.992G>A
NM_001030003.2:c.926G>A
NM_001030004.2:c.926G>A
NM_001258355.1:c.971G>A
NM_001287182.1:c.917G>A
NM_001287183.1:c.917G>A
NM_001287184.1:c.917G>A
NM_175914.4:c.926G>A
NM_178849.2:c.992G>A
NM_178850.2:c.992G>A
NM_001030003.3:c.926G>A
NM_001030004.3:c.926G>A
NM_001258355.2:c.971G>A
NM_001287182.2:c.917G>A
NM_001287184.2:c.917G>A
NM_178849.3:c.992G>A
NM_178850.3:c.992G>A
NM_000457.5:c.992G>A
NM_000457.6:c.992G>A
NM_001287183.2:c.917G>A
More

Likely Pathogenic

Met criteria codes 6
PM2_Supporting PM1_Supporting PP4 PP3 PP1_Moderate PM5_Supporting
Not Met criteria codes 3
BS1 BP4 BA1

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.926G>A variant in the hepatocyte nuclear factor 4-alpha gene, HNF4A, causes an amino acid change of arginine to histidine at codon 309 (p.(Arg309His)) of NM_175914.5. This variant is located within the ligand-binding domain (codons 180-220 and 300-350) of HNF4A, which is defined as critical for the protein’s function by the ClinGen MDEP (PM1_Supporting). This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.765, which is greater than the MDEP VCEP threshold of 0.70 (PP3). This variant has an incomputable gnomAD v2.1.1 Grpmax filtering allele frequency due to 1 copy in the South Asian subpopulation and 0 copies in any other subpopulation, thereby meeting the ClinGen MDEP threshold criteria for PM2_Supporting (ENF Grpmax FAF <= 0.000003 and <= 2 copies in ENF and <=1 copy in any other subpopulation) (PM2_Supporting). This variant was identified in an individual with a clinical history suggestive of HNF4A-MODY (neonatal hyperinsulinemic hypoglycemia and negative genetic testing for ABCC8 and KCNJ11)(PP4; internal lab contributors). This variant segregated with diabetes and/or diazoxide-responsive hyperinsulinemic hypoglycemia, with 4 informative meioses in 1 family (PP1_Moderate; internal lab contributors). Another missense variant, c.925C>T p.Arg309Cys, has been classified as pathogenic by the ClinGen MDEP but has a greater Grantham distance than p.Arg309His (PM5_Supporting). In summary, c.926G>A meets the criteria to be classified as likely pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP (specification version 2.0.0, approved 10/11/2023): PP1_Moderate, PP3, PP4, PM1_Supporting, PM2_Supporting, PM5_Supporting.
Met criteria codes
PM2_Supporting
This variant has an incomputable gnomAD v2.1.1 Grpmax filtering allele frequency due to 1 copy in the South Asian subpopulation and 0 copies in any other subpopulation, thereby meeting the ClinGen MDEP threshold criteria for PM2_Supporting (ENF Grpmax FAF <= 0.000003 and <= 2 copies in ENF and <=1 copy in any other subpopulation) (PM2_Supporting).
PM1_Supporting
This variant is located within the ligand-binding domain (codons 180-220 and 300-350) of HNF4A, which is defined as critical for the protein’s function by the ClinGen MDEP (PM1_Supporting).
PP4
This variant was identified in an individual with a clinical history suggestive of HNF4A-MODY (neonatal hyperinsulinemic hypoglycemia and negative genetic testing for ABCC8 and KCNJ11)(PP4; internal lab contributors).
PP3
This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.765, which is greater than the MDEP VCEP threshold of 0.70 (PP3).
PP1_Moderate
This variant segregated with diabetes and/or diazoxide-responsive hyperinsulinemic hypoglycemia, with 4 informative meioses in 1 family (PP1_Moderate; internal lab contributors).
PM5_Supporting
Another missense variant, c.925C>T p.Arg309Cys, has been classified as pathogenic by the ClinGen MDEP but has a greater Grantham distance than p.Arg309His (PM5_Supporting).
Not Met criteria codes
BS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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