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.724del (p.Val242fs)

CA658658870

447521 (ClinVar)

Gene: HNF4A
Condition: monogenic diabetes
Inheritance Mode: Autosomal dominant inheritance
UUID: 6ea12c74-5343-4b95-b65e-cd2df7187f02
Approved on: 2024-01-22
Published on: 2024-01-22

HGVS expressions

NM_175914.5:c.724del
NM_175914.5(HNF4A):c.724del (p.Val242fs)
NC_000020.11:g.44419774del
CM000682.2:g.44419774del
NC_000020.10:g.43048414del
CM000682.1:g.43048414del
NC_000020.9:g.42481828del
NG_009818.1:g.68974del
ENST00000316099.10:c.790del
ENST00000619550.5:c.764del
ENST00000683148.1:n.766del
ENST00000683657.1:n.1914del
ENST00000316099.9:c.790del
ENST00000316099.8:c.790del
ENST00000316673.8:c.724del
ENST00000372920.1:c.*557del
ENST00000415691.2:c.790del
ENST00000443598.6:c.790del
ENST00000457232.5:c.724del
ENST00000609795.5:c.724del
ENST00000619550.4:c.715del
NM_000457.4:c.790del
NM_001030003.2:c.724del
NM_001030004.2:c.724del
NM_001258355.1:c.769del
NM_001287182.1:c.715del
NM_001287183.1:c.715del
NM_001287184.1:c.715del
NM_175914.4:c.724del
NM_178849.2:c.790del
NM_178850.2:c.790del
NM_001030003.3:c.724del
NM_001030004.3:c.724del
NM_001258355.2:c.769del
NM_001287182.2:c.715del
NM_001287184.2:c.715del
NM_178849.3:c.790del
NM_178850.3:c.790del
NM_000457.5:c.790del
NM_000457.6:c.790del
NM_001287183.2:c.715del

Pathogenic

Met criteria codes 3
PVS1 PP4 PM2_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.724del variant in the hepatic nuclear factor 4-alpha gene, HNF4A, causes a frameshift in the protein at codon 242 in NM_175914.5, adding 39 novel amino acids before encountering a stop codon (p.(Val242Cysfs*39)). This variant, located in biologically-relevant exon 7 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 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) (PP4; internal lab contributors). In summary, c.724del 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, PP4, PM2_Supporting.
Met criteria codes
PVS1
This variant, located in biologically-relevant exon 7 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).
PP4
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) (PP4; internal lab contributors).
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting).
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