rs587777732

Positions:

• chr20-44406195-C-T

Variant summary

Our verdict is Pathogenic. Variant got 20 ACMG points: 20P and 0B. PP1_Strong PP3 PS2 PP4_Moderate PM5 PM1 PS4 PM2_Supporting

This summary comes from the ClinGen Evidence Repository: The c.187C>T variant in the hepatocyte nuclear factor 4-alpha gene, HNF4A, causes an amino acid change of arginine to tryptophan at codon 63 (p.(Arg63Trp) of NM_175914.5. This variant is absent in gnomAD v2.1.1 (PM2_Supporting), and was identified in 21 unrelated individuals with non- autoimmune and non-absolute/near-absolute insulin-deficient diabetes (PS4; PMID:24285859, 25819479, 28693455, internal lab contributors). This variant segregated with diabetes, with at least 7 meioses in 4 families (PP1_Strong, PMID:24285859, 28693455, internal lab contributors). At least 6 individuals have a clinical history highly specific for HNF4A-MODY (MODY probability calculator result >50%, negative genetic testing for HNF1A, and Fanconi phenotype) (PP4_Moderate; internal lab contributors). Additionally, this variant was identified as a de novo occurrence with both confirmed and unconfirmed parental relationships in 5 individual(s) with a clinical picture consistent with HNF4A-MODY (MODY probability calculator result >50% and negative genetic testing for HNF1A) (PS2_Very Strong; internal lab contributor, PMID:24285859, 25819479). This variant resides in an amino acid within the HNF4α DNA binding domain that directly binds DNA, which is defined as critical for the protein’s function by the ClinGen MDEP (PM1). It is also predicted to be deleterious by computational evidence, with a REVEL score of 0.949, which is greater than the MDEP VCEP threshold of 0.70 (PP3). Lastly, another missense variant, c.188G>A (p.Arg63Gln), has been interpreted as pathogenic by the ClinGen MDEP, and p.Arg63Trp has a greater Grantham distance (PM5). In summary, c.187C>T 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): PS2_Very strong, PP1_Strong, PS4, PP4_Moderate, PM1, PP3, PM2_Supporting, PM5_Supporting. LINK:https://erepo.genome.network/evrepo/ui/classification/CA170773/MONDO:0015967/085

• Frequency: Genomes: not found (cov: 33)
• Consequence: HNF4A NM_175914.5 missense
• Clinical Significance: Pathogenic reviewed by expert panel P:14
• Conservation: PhyloP100: 4.48

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]

HNF4A (HGNC:):

ACMG classification

Verdict is Pathogenic. Variant got 20 ACMG points.

• PS2: For more information check the summary or visit ClinGen Evidence Repository.
• PS4: For more information check the summary or visit ClinGen Evidence Repository.
• PM1: For more information check the summary or visit ClinGen Evidence Repository.
• PM2: For more information check the summary or visit ClinGen Evidence Repository.
• PM5: For more information check the summary or visit ClinGen Evidence Repository.
• PP1: For more information check the summary or visit ClinGen Evidence Repository.
• PP3: For more information check the summary or visit ClinGen Evidence Repository.
• PP4: For more information check the summary or visit ClinGen Evidence Repository.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HNF4A	NM_175914.5	c.187C>T	p.Arg63Trp	missense_variant	2/10	ENST00000316673.9	NP_787110.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HNF4A	ENST00000316673.9	c.187C>T	p.Arg63Trp	missense_variant	2/10	1	NM_175914.5	ENSP00000315180.4

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:14

Revision: reviewed by expert panel

Submissions by phenotype

Fanconi renotubular syndrome 4 with maturity-onset diabetes of the young Pathogenic:6

Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Sep 22, 2023	- -
Pathogenic, criteria provided, single submitter	clinical testing	Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein	Mar 18, 2021	ACMG classification criteria: PS2, PS3 supporting, PS4 moderate, PM2, PP1, PP3 -
Pathogenic, no assertion criteria provided	clinical testing	Sydney Genome Diagnostics, Children's Hospital Westmead	Dec 30, 2014	This patient is heterozygous for the c.187C>T (p.Arg63Trp) variant in the HNF4A gene. This variant has been previously described in multiple patients with Fanconi renotubular syndrome (Hamilton et al 2014 J Med Genet; 51: 165-169). -
Pathogenic, no assertion criteria provided	literature only	OMIM	Mar 01, 2014	- -
Pathogenic, criteria provided, single submitter	clinical testing	3billion	Feb 23, 2023	The variant is not observed in the gnomAD v2.1.1 dataset. Functional studies provide strong evidence of the variant having a damaging effect on the gene or gene product (PMID: 31875549). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.95; 3Cnet: 1.00). Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000156152). The variant has been observed in multiple (>3) similarly affected unrelated individuals (PMID: 20164212, 24285859, 27245055, 28458902, 28693455, 30005691, 31875549). A different missense change at the same codon (p.Arg63Gln) has been reported to be associated with HNF4A related disorder (ClinVar ID: VCV000372382 / PMID: 23348805). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline. -
Pathogenic, criteria provided, single submitter	clinical testing	Victorian Clinical Genetics Services, Murdoch Childrens Research Institute	Oct 08, 2024	Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0103 - Loss of function and dominant negative are known mechanisms of disease in this gene. Loss of function through a reduction of DNA binding is associated with MODY, type I (MIM#125850) and diabetes mellitus, noninsulin-dependent (MIM#125853) (OMIM; PMID: 31875549). Dominant negative is associated with Fanconi renotubular syndrome 4, with maturity-onset diabetes of the young (MIM#616026) (PMID: 31875549). (I) 0107 - This gene is associated with autosomal dominant disease. (I) 0112 - The condition associated with this gene has incomplete penetrance (PMID: 36257325). (I) 0200 - Variant is predicted to result in a missense amino acid change from arginine to tryptophan. (I) 0251 - This variant is heterozygous. (I) 0301 - Variant is absent from gnomAD (both v2 and v3). (SP) 0501 - Missense variant consistently predicted to be damaging by multiple in silico tools or highly conserved with a major amino acid change. (SP) 0603 - Missense variant in a region that is highly intolerant to missense variation (high constraint region in DECIPHER). (SP) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has frequently been reported as pathogenic in ClinVar and has been observed as heterozygous in multiple families and unrelated individuals with Fanconi syndrome (PMID: 24285859; PMID: 30005691). (SP) 1002 - This variant has moderate functional evidence supporting abnormal protein function (PMID:31875549). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign -

not provided Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	Athena Diagnostics	Dec 13, 2019	Not found in the total gnomAD dataset, and the data is high quality. Predicted to have a damaging effect on the protein. Found in multiple individuals with expected phenotype for this gene. Segregation with disease, and data include affected and unaffected individuals from multiple families. One de novo case with parental identity confirmed plus 2 unconfirmed cases. -
Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Nov 10, 2021	This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 63 of the HNF4A protein (p.Arg63Trp). For these reasons, this variant has been classified as Pathogenic. Experimental studies have shown that this missense change affects HNF4A function (PMID: 31875549). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). ClinVar contains an entry for this variant (Variation ID: 156152). This variant is also known as R76W and R85W. This missense change has been observed in individual(s) with hypoglycemia with hyperinsulinemia and atypical renal Fanconi syndrome (PMID: 20164212, 25819479, 28458902). In at least one individual the variant was observed to be de novo. This variant is not present in population databases (gnomAD no frequency). -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Jul 29, 2022	Published functional studies demonstrate a damaging effect for variant described as R85W, using alternate nomenclature; corresponding variant in transfected cells (Drosophila nephrocytes) showed lipid metabolism defects and mitochondrial dysfunction in a dominant-negative manner; Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Reported as R76W using alternate nomenclature; This variant is associated with the following publications: (PMID: 20164212, 22802087, 25819479, 24285859, 27245055, 28693455, 28458902, 30005691, 29493090, 31949432, 31618753, 32960281, 31216405, 33251707, 31875549) -

Type 2 diabetes mellitus;C1852093:Maturity-onset diabetes of the young type 1;C4014962:Fanconi renotubular syndrome 4 with maturity-onset diabetes of the young Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

May 11, 2024

- -

Hyperinsulinemia Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

Genetic Services Laboratory, University of Chicago

Apr 27, 2017

DNA sequence analysis of the HNF4A gene demonstrated a sequence change, c.187C>T, in exon 2 that results in an amino acid change, p.Arg63Trp. This sequence change has been described previously in a patient with hyperinsulinism, where it was inherited from a parent affected by diabetes (Flanagan et al., 2010). The c.187C>T sequence change has not been described as a known benign sequence change in the HNF4A gene. The p.Arg63Trp change affects a highly conserved amino acid residue located in a domain of the HNF4A protein that is known to be functional. The p.Arg63Trp substitution appears to be deleterious using several in-silico pathogenicity prediction tools (SIFT PolyPhen2, Align GVGD, MutationTaster). -

Monogenic diabetes Pathogenic:1

Pathogenic, reviewed by expert panel

curation

ClinGen Monogenic Diabetes Variant Curation Expert Panel

Apr 05, 2024

The c.187C>T variant in the hepatocyte nuclear factor 4-alpha gene, HNF4A, causes an amino acid change of arginine to tryptophan at codon 63 (p.(Arg63Trp) of NM_175914.5. This variant is absent in gnomAD v2.1.1 (PM2_Supporting), and was identified in 21 unrelated individuals with non- autoimmune and non-absolute/near-absolute insulin-deficient diabetes (PS4; PMID: 24285859, 25819479, 28693455, internal lab contributors). This variant segregated with diabetes, with at least 7 meioses in 4 families (PP1_Strong, PMID: 24285859, 28693455, internal lab contributors). At least 6 individuals have a clinical history highly specific for HNF4A-MODY (MODY probability calculator result >50%, negative genetic testing for HNF1A, and Fanconi phenotype) (PP4_Moderate; internal lab contributors). Additionally, this variant was identified as a de novo occurrence with both confirmed and unconfirmed parental relationships in 5 individual(s) with a clinical picture consistent with HNF4A-MODY (MODY probability calculator result >50% and negative genetic testing for HNF1A) (PS2_Very Strong; internal lab contributor, PMID: 24285859, 25819479). This variant resides in an amino acid within the HNF4alpha DNA binding domain that directly binds DNA, which is defined as critical for the protein’s function by the ClinGen MDEP (PM1). It is also predicted to be deleterious by computational evidence, with a REVEL score of 0.949, which is greater than the MDEP VCEP threshold of 0.70 (PP3). Lastly, another missense variant, c.188G>A (p.Arg63Gln), has been interpreted as pathogenic by the ClinGen MDEP, and p.Arg63Trp has a greater Grantham distance (PM5). In summary, c.187C>T 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): PS2_Very strong, PP1_Strong, PS4, PP4_Moderate, PM1, PP3, PM2_Supporting, PM5_Supporting. -

Maturity onset diabetes mellitus in young Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Mar 05, 2019

The p.R63W pathogenic mutation (also known as c.187C>T, p.R85W, and p.R76W), located in coding exon 2 of the HNF4A gene, results from a C to T substitution at nucleotide position 187. The arginine at codon 63 is replaced by tryptophan, an amino acid with dissimilar properties. This mutation has been detected in individuals with diazoxide responsive hyperinsulinemic hypoglycemia (HH), Fanconi syndrome, nephrocalcinosis, congenital hyperinsulinism (CHI) and hypoglycemia (Flanagan SE et al. Eur. J. Endocrinol., 2010 May;162:987-92; Hamilton AJ et al. J. Med. Genet., 2014 Mar;51:165-9; Numakura C et al. Diabetes Res. Clin. Pract., 2015 Jun;108:e53-5; Walsh SB et al. BMC Nephrol, 2017 Jul;18:230). In addition, this mutation has been detected as de novo occurrences (paternity not confirmed) in one individual with hyperinsulinism, hepatomegaly, macrosomia, and renal Fanconi syndrome (Stanescu DE et al. J. Clin. Endocrinol. Metab., 2012 Oct;97:E2026-30), in another with hyperinsulinaemic hypoglycaemia and renal tubulopathy (Clemente M et al. Endocrinol Diabetes Metab Case Rep, 2017 Mar;2017:), and in one with Fanconi syndrome, infantile hyperinsulinemic hypoglycemia, transient cholestasis, and bilateral severe hearing loss. (Liu J et al. J Med Case Rep, 2018 Jul;12:203). A different alteration located at the same position, p.R63Q, has been detected in two families with maturity-onset diabetes of the young (MODY); however, specific phenotypic info was not provided (Colclough K et al. Hum. Mutat., 2013 May;34:669-85). In addition, based on internal structural analysis, this variant is more disruptive than known pathogenic variants nearby. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -

Maturity-onset diabetes of the young type 1;C4014962:Fanconi renotubular syndrome 4 with maturity-onset diabetes of the young Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Baylor Genetics

Dec 31, 2017

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	1.0
BayesDel_addAF	Pathogenic	0.53	D
BayesDel_noAF	Pathogenic	0.52
CADD	Pathogenic	34
DANN	Pathogenic	1.0
DEOGEN2	Uncertain	0.61	.;.;.;D;D;.;D;.
Eigen	Pathogenic	0.86
Eigen_PC	Pathogenic	0.71
FATHMM_MKL	Uncertain	0.82	D
LIST_S2	Uncertain	0.97	D;D;D;D;D;D;D;D
M_CAP	Pathogenic	0.94	D
MetaRNN	Pathogenic	0.99	D;D;D;D;D;D;D;D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Pathogenic	3.6	.;.;.;.;.;H;H;H
PrimateAI	Pathogenic	0.93	D
PROVEAN	Pathogenic	-7.0	D;.;D;.;.;D;D;D
REVEL	Pathogenic	0.95
Sift	Pathogenic	0.0	D;.;D;.;.;D;D;D
Sift4G	Pathogenic	0.0	D;D;D;D;D;D;D;D
Polyphen		1.0	.;D;D;.;.;D;D;.
Vest4		0.97
MutPred		0.91		.;.;.;.;.;Loss of disorder (P = 4e-04);Loss of disorder (P = 4e-04);Loss of disorder (P = 4e-04);
MVP		0.99
MPC		2.6
ClinPred		1.0	D
GERP RS		4.2
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		2.7
Varity_R		0.88
gMVP		0.96

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: rs587777732; hg19: chr20-43034835; COSMIC: COSV57388402; COSMIC: COSV57388402;