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.1del (p.Met1fs)

CA2499225757

1299752 (ClinVar)

Gene: HNF4A
Condition: monogenic diabetes
Inheritance Mode: Autosomal dominant inheritance
UUID: e04246bc-5146-4ac3-b0aa-d74f0d62937d
Approved on: 2024-04-06
Published on: 2024-04-06

HGVS expressions

NM_175914.5:c.1del
NM_175914.5(HNF4A):c.1del (p.Met1fs)
NC_000020.11:g.44355805del
CM000682.2:g.44355805del
NC_000020.10:g.42984445del
CM000682.1:g.42984445del
NC_000020.9:g.42417859del
NG_009818.1:g.5005del
ENST00000316673.9:c.1del
ENST00000316673.8:c.1del
ENST00000457232.5:c.1del
ENST00000609262.5:c.-231del
ENST00000609795.5:c.1del
ENST00000619550.4:c.-231del
NM_001030003.2:c.1del
NM_001030004.2:c.1del
NM_001287182.1:c.-231del
NM_001287183.1:c.-231del
NM_001287184.1:c.-231del
NM_175914.4:c.1del
NM_001030003.3:c.1del
NM_001030004.3:c.1del
NM_001287182.2:c.-231del
NM_001287184.2:c.-231del
NM_001287183.2:c.-231del
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Likely Pathogenic

Met criteria codes 4
PM2_Supporting PP1 PVS1_Strong PP4_Moderate

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.1del variant in the hepatic nuclear factor 4-alpha gene, HNF4A, results in the loss of the initiation codon (p.Met1?) of NM_175914.5. By altering the start codon of the coding sequence, this variant may cause a truncated or absent protein in a gene in which loss-of-function is an established disease mechanism (PMID: 23348805).This variant is absent from gnomAD v2.1.1 (PM2_Supporting). This variant was identified in an individual with a clinical history highly specific for HNF4A-MODY (MODY probability calculator result >50%, negative genetic testing for HNF1A, and sulfonylurea responsive) (PP4_Moderate; Internal lab contributor). This variant segregated with diabetes, with three informative meioses in one family (PP1; Internal lab contributors). In summary, c.1del 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 10/11/1024): PVS1_Strong, PP4_Moderate, PP1, PM2_Supporting.
Met criteria codes
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting).
PP1
This variant segregated with diabetes, with three informative meioses in one family with MODY (PP1; Internal lab contributors).
PVS1_Strong
By altering the start codon of the coding sequence, this variant may cause a truncated or absent protein in a gene in which loss-of-function is an established disease mechanism (PMID: 23348805).
PP4_Moderate
This variant was identified in an individual with a clinical history highly specific for HNF4A-MODY (MODY probability calculator result >50%, negative genetic testing for HNF1A, and sulfonylurea responsive) (PP4_Moderate; Internal lab contributor).
Curation History
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