ClinVar Genomic variation as it relates to human health

The c.335G>A variant in the hepatic nuclear factor 4-alpha gene, HNF4A, causes an amino acid change of arginine to glutamine at codon 112 (p.(Arg112Gln)) of NM_175914.5. This variant resides in an amino acid within the HNF4A DNA binding domain that directly binds DNA, which is defined as critical for the protein’s function by the ClinGen MDEP (PM1). This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.959, which is greater than the MDEP VCEP threshold of 0.70 (PP3). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). This variant was identified in at least 17 unrelated individuals with non-autoimmune and non-absolute/near-absolute insulin-deficient diabetes (PS4; PMIDs: 36257325, 25306193, 26552609, 18356407, internal lab contributors). At least one of these individuals had 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 contributors). This variant segregated with diabetes, with 12 informative meioses in 11 families (PP1_Strong; PMID: 18356407, internal lab contributors). Another missense variant, c.334C>T p.Arg112Trp, has been classified as pathogenic by the ClinGen MDEP but has a greater Grantham distance than p.Arg112Gln (PM5_Supporting). In summary, c.335A>G meets the criteria to be classified as pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP (specification version 1.1.0, approved 8/11/2023): PS4, PP1_Strong, PM1, PP4_Moderate, PP3, PM2_Supporting, PM5_Supporting.

PS4, PP1_Strong, PP4_Moderate, PM2, PP3, PM1, PM5_Supporting

Variant summary: HNF4A c.335G>A (p.Arg112Gln) results in a conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 250614 control chromosomes. c.335G>A has been reported in the literature in individuals affected with Maturity Onset Diabetes of the Young 1 (MODY1)/Neonatal Diabetes Mellitus (e.g. Harries_2008, Alkorta-Aranburu_2014, Hamilton_2014, Sztromwasser_2020, Colcough_2022, Dusatkova_2022). These data indicate that the variant is very likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 25306193, 34789499, 24285859, 18356407, 31825128). Five submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. All submitters classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 112 of the HNF4A protein (p.Arg112Gln). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with clinical features of maturity-onset diabetes of the young (PMID: 18356407, 26552609, 31825128; external communication). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 427034). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on HNF4A protein function. For these reasons, this variant has been classified as Pathogenic.

Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 23348805, 31825128, 36257325, 33149276, 26552609, 25306193, 34789499, 18356407, 36208030, 18829458, 38733153)

This variant has been identified in multiple unrelated individuals with clinical features associated with this gene. This variant has not been reported in large, multi-ethnic general populations. (http://gnomad.broadinstitute.org) In some published literature, this variant is referred to as c.335G>A (p.Arg112Gln) or c.374G>A (p.Arg125Gln).

DNA sequence analysis of the HNF4A gene demonstrated a sequence change, c.335G>A, in exon 4 that results in an amino acid change, p.Arg112Gln. The p.Arg112Gln change affects a highly conserved amino acid residue located in a domain of the HNF4A protein that is known to be functional. In-silico pathogenicity prediction tools (SIFT, PolyPhen2, Align GVGD, REVEL) provide contradictory results for the p.Arg112Gln substitution. This sequence change has been described in individuals with MODY and renal cysts (PMID: 26552609, 18356407, 31825128). This sequence change has not been described in population databases such as ExAC and gnomAD. This sequence change is the likely cause of this individual's phenotype, however functional studies have not been performed to prove this conclusively.