The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]


Variant: NM_175914.5(HNF4A):c.48C>G (p.Tyr16Ter)

CA409109938

1299754 (ClinVar)

Gene: HNF4A
Condition: monogenic diabetes
Inheritance Mode: Autosomal dominant inheritance
UUID: fd68f169-099f-4a0b-ac50-cd155261b31b
Approved on: 2024-01-22
Published on: 2024-01-22

HGVS expressions

NM_175914.5:c.48C>G
NM_175914.5(HNF4A):c.48C>G (p.Tyr16Ter)
NC_000020.11:g.44355852C>G
CM000682.2:g.44355852C>G
NC_000020.10:g.42984492C>G
CM000682.1:g.42984492C>G
NC_000020.9:g.42417906C>G
NG_009818.1:g.5052C>G
ENST00000316673.8:c.48C>G
ENST00000457232.5:c.48C>G
ENST00000609262.5:c.-184C>G
ENST00000609795.5:c.48C>G
ENST00000619550.4:c.-184C>G
NM_001030003.2:c.48C>G
NM_001030004.2:c.48C>G
NM_001287182.1:c.-184C>G
NM_001287183.1:c.-184C>G
NM_001287184.1:c.-184C>G
NM_175914.4:c.48C>G
NM_001030003.3:c.48C>G
NM_001030004.3:c.48C>G
NM_001287182.2:c.-184C>G
NM_001287184.2:c.-184C>G
NM_001287183.2:c.-184C>G
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Pathogenic

Met criteria codes 4
PM2_Supporting PP4_Moderate PVS1 PP1_Strong
Not Met criteria codes 1
PS4

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.48C>G variant in the hepatic nuclear factor 4-alpha gene, HNF4A, results in a premature termination at codon 16 (p.(Tyr16*)) of NM_175914.5. This variant, located in biologically-relevant exon 1 of 10, is predicted to lead to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism (PVS1; PMID: 23348805). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). This variant segregated with diabetes/neonatal hyperinsulinism, with 13 informative meioses in 2 families (PP1_Strong; internal lab contributors). This variant was identified in 3 unrelated individuals with non-autoimmune and non-absolute/near-absolute insulin-deficient diabetes or diazoxide-responsive hyperinsulinemic hypoglycemia; however, PS4 cannot be applied because this number is below the ClinGen MDEP threshold (PMIDs: 20164212, 16917892, 17407387, 18268044, internal lab contributors). One of these individuals had a clinical history highly specific for HNF4A-monogenic diabetes (MODY probability calculator result >50%, negative genetic testing for HNF1A, and sulfonylurea-responsive) (PP4_Moderate; internal lab contributors). In summary, c.48C>G 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): PVS1, PP1_Strong, PP4_Moderate, PM2_Supporting.
Met criteria codes
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting).
PP4_Moderate
This variant was identified in an individual with a clinical history highly specific for HNF4A-monogenic diabetes (MODY probability calculator result >50%, negative genetic testing for HNF1A, and sulfonylurea-responsive) (PP4_Moderate; internal lab contributors).
PVS1
This variant, located in biologically-relevant exon 1 of 10, is predicted to lead to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism (PVS1; PMID: 23348805).
PP1_Strong
This variant segregated with diabetes/neonatal hyperinsuliinsm, with 13 informative meioses in 2 families (PP1_Strong; internal lab contributors).
Not Met criteria codes
PS4
This variant was identified in 3 unrelated individuals with non-autoimmune and non-absolute/near-absolute insulin-deficient diabetes or diazoxide-responsive hyperinsulinemic hypoglycemia; however, PS4 cannot be applied because this number is below the ClinGen MDEP threshold (PMIDs: 20164212, 16917892, 17407387, 18268044, internal lab contributors).
Curation History
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