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 label mismatch: HNF4A vs undefined
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computed assertion could be determined for this classification!


Variant: NM_175914.5(HNF4A):c.1321A>G (p.Ile441Val)

CA213913

36345 (ClinVar)

Gene: HNF4A
Condition: monogenic diabetes
Inheritance Mode: Autosomal dominant inheritance
UUID: a2587a88-8193-4949-94fa-a8203f614da4
Approved on: 2025-06-09
Published on: 2025-06-09

HGVS expressions

NM_175914.5:c.1321A>G
NM_175914.5(HNF4A):c.1321A>G (p.Ile441Val)
NC_000020.11:g.44429627A>G
CM000682.2:g.44429627A>G
NC_000020.10:g.43058267A>G
CM000682.1:g.43058267A>G
NC_000020.9:g.42491681A>G
NG_009818.1:g.78827A>G
ENST00000316673.9:c.1321A>G
ENST00000316099.10:c.1387A>G
ENST00000316099.9:c.1387A>G
ENST00000316099.8:c.1387A>G
ENST00000316673.8:c.1321A>G
ENST00000372920.1:c.*1154A>G
ENST00000415691.2:c.1357A>G
ENST00000457232.5:c.1291A>G
ENST00000619550.4:c.1312A>G
NM_000457.4:c.1387A>G
NM_001030003.2:c.1291A>G
NM_001258355.1:c.1366A>G
NM_001287182.1:c.1282A>G
NM_001287183.1:c.1312A>G
NM_175914.4:c.1321A>G
NM_178849.2:c.1357A>G
NM_001030003.3:c.1291A>G
NM_001258355.2:c.1366A>G
NM_001287182.2:c.1282A>G
NM_178849.3:c.1357A>G
NM_000457.5:c.1387A>G
NM_000457.6:c.1387A>G
NM_001287183.2:c.1312A>G
More

Benign

Met criteria codes 5
BP5 PP4_Moderate BA1 BS4 BS3_Supporting
Not Met criteria codes 4
BP4 PS4 PP3 PM1

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.1321A>G variant in the hepatocyte nuclear factor 4-alpha gene, HNF4A, causes an amino acid change of isoleucine to valine at codon 441 (p.(Ile441Val)) of NM_175914.4. This variant has a Grpmax Filtering allele frequency in gnomAD 2.1.1 of 0.0005025, which is greater than the MDEP threshold for BA1 (BA1). 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 GAD negative) (PP4_Moderate, internal contributors). There is evidence in vitro that this variant has identical transactivation activity to wildtype, indicating that this variant does not impact protein function (BS3_Supporting, PMID: 30191603). This variant does not segregate with diabetes in three families (BS4; internal lab contributors, PMIDs: 25905084, 10227563, 33324081). This variant was identified in a patient with an alternate molecular basis for disease (BP5; internal lab contributors). This variant has a REVEL score of 0.354, which is between the ClinGen MDEP thresholds for BP4 and PP3, predicting neither a damaging nor benign impact on HNF1A function. In summary, c.1321A>G p.(Ile441Val) meets the criteria to be classified as benign for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP VCEP (specification version 2.0.0, approved 10/11/2023): BA1, PP4_Moderate, BS3_Supporting, BS4, BP5.
Met criteria codes
BP5
This variant was identified in a patient with an alternate molecular basis for disease (BP5; internal lab contributors).
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 GAD negative) (PP4_Moderate, internal contributors).
BA1
Grpmax Filtering allele frequency in gnomAD v2.1.1 of 0.0005025, which is greater than the MDEP threshold for BA1 (0.0001) (BA1).
BS4
This variant did not segregate with diabetes in three families (BS4; internal lab contributors, PMIDs: 25905084, 10227563, 33324081).
BS3_Supporting
There is evidence in vitro that this variant has identical transactivation activity to wildtype, indicating that this variant does not impact protein function (BS3_Supporting, PMID: 30191603).
Not Met criteria codes
BP4
This variant has a REVEL score of 0.354, which is between the ClinGen MDEP thresholds for BP4 and PP3, predicting neither a damaging nor benign impact on HNF1A function.
PS4
Cannot be applied because PM2_Supporting is not met.
PP3
This variant has a REVEL score of 0.354, which is between the ClinGen MDEP thresholds for BP4 and PP3, predicting neither a damaging nor benign impact on HNF1A function.
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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