chr20-44424123-G-A

Position:

• chr20-44424123-G-A

Variant summary

Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PM5_Supporting PP4_Moderate PP3 PM2_Supporting PS4 PM1_Supporting PP1_Strong

This summary comes from the ClinGen Evidence Repository: The c.932G>A variant in the hepatocyte nuclear factor 4 alpha gene, HNF4A, causes an amino acid change of arginine to histidine at codon 311 (p.(Arg311His)) of NM_175914.5. This variant has an incomputable gnomAD v2.1.1 Grpmax filtering allele frequency due to absence in the European non-Finnish subpopulation and 1 copy in the East Asian subpopulation, thereby meeting the ClinGen MDEP threshold criteria for PM2_Supporting (ENF GrpmaxPopmax FAF <= 0.000003 and <= 2 copies in ENF and <=1 copy in any other subpopulation) (PM2_Supporting). This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.91​, which is greater than the MDEP VCEP threshold of 0.70 (PP3). This variant is located within the ligand-binding domain (codons 300-350) of HNF4A, which is defined as critical for the protein's function by the ClinGen MDEP (PM1_Supporting). This variant was identified in 7 unrelated individuals with non-autoimmune and non-absolute/near-absolute insulin-deficient diabetes (PS4; PMID:25414397, 24947580 26059258, 32533152; internal lab contributors). This variant was identified in at least two individuals with a clinical history highly specific for HNF4A-MODY monogenic diabetes (MODY probability calculator result >50%, negative genetic testing for HNF1A, and negative antibodies; and family history of LGA/hypoglycemic infant) (PP4_Moderate; PMID:24947580, internal lab contributors). This variant segregated with diabetes, with 12 informative meioses in 4 families (PP1_Strong; PMIDs: 24947580, 26059258, 32533152, internal lab contributors). Another missense variant, p.(Arg311Cys), has been classified as pathogenic by the ClinGen MDEP but has a greater Grantham distance than p.(Arg311His) (PM5_Supporting). In summary, c.932G>A meets the criteria to be classified as pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP VCEP (specification version 2.0.0, approved 10/11/2023): PM2_Supporting, PP3, PM1_Supporting, PS4, PP4_Moderate, PP1_Strong, PM5_Supporting. LINK:https://erepo.genome.network/evrepo/ui/classification/CA409108268/MONDO:0015967/085

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000034 (0 hom.)
• Consequence: HNF4A NM_175914.5 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:6 U:4
• Conservation: PhyloP100: 10.0

Genes affected

HNF4A (HGNC:5024): (hepatocyte nuclear factor 4 alpha) The protein encoded by this gene is a nuclear transcription factor which binds DNA as a homodimer. The encoded protein controls the expression of several genes, including hepatocyte nuclear factor 1 alpha, a transcription factor which regulates the expression of several hepatic genes. This gene may play a role in development of the liver, kidney, and intestines. Mutations in this gene have been associated with monogenic autosomal dominant non-insulin-dependent diabetes mellitus type I. Alternative splicing of this gene results in multiple transcript variants encoding several different isoforms. [provided by RefSeq, Apr 2012]

ACMG classification

Verdict is Pathogenic. Variant got 14 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HNF4A	NM_175914.5	c.932G>A	p.Arg311His	missense_variant	8/10	ENST00000316673.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HNF4A	ENST00000316673.9	c.932G>A	p.Arg311His	missense_variant	8/10	1	NM_175914.5

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD3 exomes AF: 0.00000402 AC: 1 AN: 248800 Hom.: 0 AF XY: 0.00000741 AC XY: 1 AN XY: 134936

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.0000545

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000342 AC: 5 AN: 1461130 Hom.: 0 Cov.: 32 AF XY: 0.00000413 AC XY: 3 AN XY: 726854

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000448

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000252

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000180

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

Bravo AF: 0.00000756

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:6 Uncertain:4

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Maturity-onset diabetes of the young type 1 Pathogenic:3 Uncertain:1

Likely pathogenic, criteria provided, single submitter	research	Department Of Endocrinology, Sanjay Gandhi Postgraduate Institute Of Medical Sciences	Aug 15, 2023	A heterozygous missense variation in exon 8 of the HNF4A gene (chr20:g.43052763G>A) that results in the amino acid substitution of Histidine for Arginine at codon 333. The observed variation lies in the ligand-binding domain of the HNF4A protein and has previously been reported in patients affected with MODY (eg. PMID: 26059258, 25414397, 24947580). The in silico predictions of the variant are probably damaging by PolyPhen-2, and damaging by SIFT and MutationTaster2. The reference codon is conserved across species. The p.Arg333His variant has not been reported in the 1000 genomes and gnomAD. The variant was found to co-segregate with early onset diabetes mellitus in the family tested. PM1, PM2, PP1, PP3, PP5 -
Uncertain significance, criteria provided, single submitter	curation	Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard	Jan 22, 2020	The p.Arg333His variant in HNF4A has been reported in at least 3 individuals with maturity-onset diabetes of the young type 1 (MODY1) (PMID: 24947580, 25414397, 26059258) and has been Identified in 0.005451% (1/18346) of East Asian chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs1375557127). In vitro functional studies demonstrating reduced relative activity in cells transfected with the variant provide some evidence that the p.Arg333His variant may slightly impact protein function (PMID: 23485969). However, these types of assays may not accurately represent biological function. Computational prediction tools and conservation analyses suggest that this variant may impact the protein, though this information is not predictive enough to determine pathogenicity. The p.Arg333His variant is located in a region of HNF1A that is essential to ligand binding and stability, suggesting that this variant is in a functional domain and slightly supports pathogenicity (PMID: 23485969). In summary, while there is some suspicion for a pathogenic role, the clinical significance of this variant is uncertain. ACMG/AMP Criteria applied: BS1, PM2, PP3, PS4_supporting, PS3_supporting, PM1_supporting (Richards 2015). -
Pathogenic, criteria provided, single submitter	clinical testing	Translational Genomics Laboratory, University of Maryland School of Medicine	Oct 19, 2017	The c.923G>A variant in codon 308 (exon 10) of the Hepatocyte Nuclear Factor 4-Alpha gene, HNF4A, results in the substitution of Arginine to Histidine. Missense mutations in the HNF4A gene, including ones in exon 10, have been reported previously in patients with a clinical picture consistent with Maturity-Onset Diabetes of the Young, Type 1 (MODY1) (23348805). The c.923G>A variant was not observed in the NHLBI Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium databases; however, the c.923G>A variant has been previously identified in multiple individuals with a diagnosis of MODY1 (10768098, 24947580, 26059258), with evidence of co-segregation in three families (24947580, K. Colclough, personal communication, January 3rd, 2017). Different amino acid substitutions at Arg308 (Arg308Cys and Arg308Ser) have been identified in patients with a strong MODY1 phenotype and have shown co-segregation in one family (K. Colclough, personal communication, January 3rd, 2017). Additionally, multiple lines of computational evidence (SIFT, Polyphen, MutationTaster, FATHMM, MetaSVM, MetalR, Provean, GERP, CADD) predict this variant is probably damaging to the protein structure, function, or protein-protein interaction. The c.923G>A variant is located in the ligand-binding domain of the protein, a region of the protein that has minimal benign variation among individuals in population databases and in the literature (23485969, 16917892). ACMG criteria = PP1-strong, PM1, PM2, PM5, PP3 -
Likely pathogenic, criteria provided, single submitter	research	Geisinger Clinic, Geisinger Health System	Aug 02, 2022	PM2, PP3, PM5, PP4, PM1_Supporting -

not provided Pathogenic:1 Uncertain:2

Likely pathogenic, criteria provided, single submitter	clinical testing	Invitae	Apr 24, 2023	In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. This variant disrupts the p.Arg311 amino acid residue in HNF4A. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 28862987, 36257325). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. Experimental studies have shown that this missense change does not substantially affect HNF4A function (PMID: 12110948). 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. ClinVar contains an entry for this variant (Variation ID: 586023). This variant is also known as R324H. This missense change has been observed in individuals with maturity onset diabetes of the young (PMID: 25414397, 36257325). This variant is present in population databases (no rsID available, gnomAD 0.006%). This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 311 of the HNF4A protein (p.Arg311His). -
Uncertain significance, criteria provided, single submitter	clinical testing	Athena Diagnostics	Nov 22, 2017	- -
Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Jan 12, 2022	Not observed at a 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: 26059258, 24947580, 10768098, 32533152, 23348805, 16917892, 12110948, 25414397) -

Maturity onset diabetes mellitus in young Pathogenic:2

Likely pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Mar 07, 2019	The p.R311H variant (also known as c.932G>A), located in coding exon 8 of the HNF4A gene, results from a G to A substitution at nucleotide position 932. The arginine at codon 311 is replaced by histidine, an amino acid with highly similar properties. This variant was identified in several individuals with a maturity -onset diabetes of the young (MODY) phenotype (Price JA et al. Diabetologia, 2000 Mar;43:364-72; Delvecchio M et al. Ital J Pediatr, 2014 Jun;40:58; Chambers C et al. Pediatr Diabetes, 2016 08;17:360-7) and was shown to segregate with diabetes and impaired glucose tolerance in one family (Delvecchio M et al. Ital J Pediatr, 2014 Jun;40:58). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the majority of available evidence to date, this variant is likely to be pathogenic. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Nov 06, 2020	The p.Arg326His (p.Arg333His) variant in HNF4A has been reported in at least 1 individual with type II diabetes (Price PMID: 10768098) and in 3 children with maturity-onset diabetes of the young, segregating with hyperglycemia (albeit different phenotypes) in at least 4 relatives from 2 families (Delvecchio 2014 PMID: 24947580), Delvecchio 2014 PMID: 25414397, Chambers 2016 PMID: 26059258). It has also been reported in ClinVar (Variation ID: 586023). It has been identified in 0.005% (1/18346) of East Asian chromosomes by gnomAD (http://gnomad.broadinstitute.org). Computational prediction tools and conservation analyses suggest that this variant may impact the protein, though this information is not predictive enough to determine pathogenicity. In vitro functional studies provide some evidence that this variant may impact protein function (Chandra 2013 PMID: 23485969). However, these types of assays may not accurately represent biological function. The p.Arg333His variant is located in a region of HNF4A that is essential to ligand binding and stability (Chandra 2013 PMID: 23485969). In summary although additional studies are required to fully establish its clinical significance, this variant meets criteria to be classified as likely pathogenic for autosomal dominant maturity onset diabetes of the young (MODY). ACMG/AMP Criteria applied: PM2, PP3,PP1, PS4_Supporting, PS3_Supporting, PM1_Supporting. -

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Mar 22, 2023

Variant summary: HNF4A c.932G>A (p.Arg311His) results in a non-conservative amino acid change located in the Nuclear hormone receptor, ligand-binding domain (IPR000536) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 4e-06 in 248800 control chromosomes. c.932G>A has been reported in the literature as segregating with a clinically heterogeneous phenotype of MODY in at-least one family, in studies of subjects reporting diabetic nephropathy and studies reporting a clinically characterized phenotype of MODY with subsequent citations by others (example, PMID: 32533152, 26059258, 25414397, 24947580, 29355436, 36227502, 10768098). The original clinically heterogeneous family included a proband with MODY, a brother with Impaired glucose tolerance at a young age (8 y), a mother with gestational diabetes and a maternal uncle with type 2 DM diagnosed at age 30 (PMID: 25414397, 24947580). These data indicate that the variant may be associated with disease. At least two publications report experimental evidence evaluating an impact on protein function (example, PMID: 16640558, 12110948). These results showed no damaging effect of this variant. Seven clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Multiple laboratories reported the variant with conflicting assessments while citing overlapping evidence utilized in the context of this evaluation (P/LP, n=3; VUS, n=4). Based on the evidence outlined above, the variant was classified as VUS-possibly pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.77
BayesDel_addAF	Pathogenic	0.41	D
BayesDel_noAF	Pathogenic	0.52
CADD	Pathogenic	33
DANN	Pathogenic	1.0
DEOGEN2	Uncertain	0.52	.;.;.;D;.;D;.
Eigen	Pathogenic	0.86
Eigen_PC	Pathogenic	0.82
FATHMM_MKL	Uncertain	0.97	D
LIST_S2	Pathogenic	0.99	D;D;D;D;D;D;D
M_CAP	Pathogenic	0.59	D
MetaRNN	Pathogenic	0.99	D;D;D;D;D;D;D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Pathogenic	3.0	.;.;.;.;M;M;M
MutationTaster	Benign	1.0	D;D;D;D;D
PrimateAI	Pathogenic	0.88	D
PROVEAN	Uncertain	-4.0	D;.;D;.;D;D;D
REVEL	Pathogenic	0.91
Sift	Uncertain	0.025	D;.;D;.;D;D;D
Sift4G	Benign	0.064	T;T;T;T;T;T;T
Polyphen		1.0, 1.0, 1.0, 1.0	.;D;D;.;D;D;.
Vest4		0.93
MutPred		0.97		.;.;.;.;Loss of methylation at R333 (P = 0.0148);Loss of methylation at R333 (P = 0.0148);Loss of methylation at R333 (P = 0.0148);
MVP		0.99
MPC		1.1
ClinPred		0.99	D
GERP RS		5.4
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.68
gMVP		0.89

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1375557127; hg19: chr20-43052763; COSMIC: COSV57386667;