rs587780357

chr12-120993601-G-Achr12-120993601-G-Cchr12-120993601-G-T

Variant summary

Our verdict is Pathogenic. Variant got 20 ACMG points: 20P and 0B. PS1_ModeratePM1PM2PM5PP3_StrongPP5_Very_Strong

The NM_000545.8(HNF1A):c.608G>A(p.Arg203His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,880 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 11/19 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely pathogenicin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R203C) has been classified as Pathogenic.

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 0.0000014 ( 0 hom. )

Consequence

HNF1A
NM_000545.8 missense

Scores

Clinical Significance

Pathogenic reviewed by expert panel P:8

Conservation

PhyloP100: 9.42

Variant links:

Genes affected

HNF1A (HGNC:11621): (HNF1 homeobox A) The protein encoded by this gene is a transcription factor required for the expression of several liver-specific genes. The encoded protein functions as a homodimer and binds to the inverted palindrome 5'-GTTAATNATTAAC-3'. Defects in this gene are a cause of maturity onset diabetes of the young type 3 (MODY3) and also can result in the appearance of hepatic adenomas. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Apr 2015]

HNF1A links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 20 ACMG points.

PS1

Transcript NM_000545.8 (HNF1A) is affected with MISSENSE_VARIANT having same AA change as one Pathogenic present in UniProt

PM1

In a hotspot region, there are 4 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 1 benign, 3 uncertain in NM_000545.8

PM2

Very rare variant in population databases, with high coverage;

PM5

Other missense variant is known to change same aminoacid residue: Variant chr12-120993600-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 1338381.Status of the report is reviewed_by_expert_panel, 3 stars.

PP3

MetaRNN computational evidence supports a deleterious effect, 0.981

PP5

Variant 12-120993601-G-A is Pathogenic according to our data. Variant chr12-120993601-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 129235.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr12-120993601-G-A is described in Lovd as [Pathogenic]. Variant chr12-120993601-G-A is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
HNF1A	NM_000545.8 linkuse as main transcript	c.608G>A	p.Arg203His	missense_variant	3/10	ENST00000257555.11
HNF1A	NM_001306179.2 linkuse as main transcript	c.608G>A	p.Arg203His	missense_variant	3/10
HNF1A	NM_001406915.1 linkuse as main transcript	c.608G>A	p.Arg203His	missense_variant	3/9
HNF1A	XM_024449168.2 linkuse as main transcript	c.608G>A	p.Arg203His	missense_variant	3/9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HNF1A	ENST00000257555.11 linkuse as main transcript	c.608G>A	p.Arg203His	missense_variant	3/10	1	NM_000545.8	P4

Frequencies

GnomAD3 genomes

Cov.:

GnomAD3 exomes

AF:

0.00000796

AC:

AN:

251318

Hom.:

AF XY:

0.00000736

AC XY:

AN XY:

135870

show subpopulations

Gnomad AFR exome

AF:

0.0000616

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00000880

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00000137

AC:

AN:

1461880

Hom.:

Cov.:

AF XY:

0.00000138

AC XY:

AN XY:

727242

show subpopulations

Gnomad4 AFR exome

AF:

0.0000299

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

8.99e-7

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:8

Revision: reviewed by expert panel

LINK: link

Submissions by phenotype

not provided

Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Nov 10, 2023	This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 203 of the HNF1A protein (p.Arg203His). This variant is present in population databases (rs587780357, gnomAD 0.007%). This missense change has been observed in individuals with clinical features of maturity-onset diabetes of the young (PMID: 10588527, 12627330, 15928245, 30293189). ClinVar contains an entry for this variant (Variation ID: 129235). 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 HNF1A protein function. Experimental studies have shown that this missense change affects HNF1A function (PMID: 16274290). This variant disrupts the p.Arg203 amino acid residue in HNF1A. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 21168233, 30293189, 31363388; Invitae). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Mar 06, 2023	A different missense change at this residue (p.(R203C)) has been reported as pathogenic in the published literature and at GeneDx in association with MODY (Lopez et al., 2011; Plengvidhya et al., 2019); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Classified as pathogenic by the ClinGen Monogenic Diabetes Expert Panel (ClinVar SCV002499516.1); This variant is associated with the following publications: (PMID: 18003757, 12488961, 15657605, 11772903, 23274891, 16274290, 15928245, 27271189, 23348805, 12453420, 10588527, 12627330, 30293189, 33046911, 32910913, 33950347, 35673428, 36257325, 33477506, 35921062, 21168233, 27913849, 31363388) -
Pathogenic, criteria provided, single submitter	clinical testing	Athena Diagnostics	Jul 18, 2022	The frequency of this variant in the general population is consistent with pathogenicity (http://gnomad.broadinstitute.org). This variant has been identified in multiple unrelated individuals with clinical features associated with MODY. This variant is statistically more frequent in affected individuals than in the general population and/or healthy controls. Assessment of experimental evidence suggests this variant results in abnormal protein function. The variant is located in a region that is considered important for protein function and/or structure. -

Maturity onset diabetes mellitus in young

Pathogenic:2

Pathogenic, criteria provided, single submitter	research	Clinical Genomics, Uppaluri K&H Personalized Medicine Clinic	-	Mutations in HNF1A gene can predispose to MODY3. It is associated with both micro and macrovascular complications of diabetes, especially cardiovascular complications. Associated with glucosuria. May respond well to sulfonylureas. Sufficient evidence is found to confer the association of this particular variant rs587780357 with MODY3. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Apr 07, 2021	The p.R203H variant (also known as c.608G>A), located in coding exon 3 of the HNF1A gene, results from a G to A substitution at nucleotide position 608. The arginine at codon 203 is replaced by histidine, an amino acid with highly similar properties. This variant has been reported in multiple individuals and families with features of maturity-onset diabetes of the young (Thanabalasingham G et al. Diabetes, 2013 Apr;62:1329-37; Shepherd M et al. Diabetes Care, 2016 Nov;39:1879-1888; Bansal V et al. BMC Med, 2017 12;15:213; Johansson BB et al. Diabetologia, 2017 04;60:625-635; Bonnefond A et al. Nat Metab, 2020 10;2:1126-1134; Ivanoshchuk DE et al. J Pers Med, 2021 Jan;11:). Based on internal structural analysis, this variant is mildly destabilizing to the local structure (Chi YI et al. Mol Cell, 2002 Nov;10:1129-37; P S et al. PLoS One, 2017 Apr;12:e0174953). 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. -

Monogenic diabetes

Pathogenic:1

Pathogenic, reviewed by expert panel

curation

ClinGen Monogenic Diabetes Variant Curation Expert Panel

Apr 10, 2022

The c.608G>A variant in the HNF1 homeobox A gene, HNF1A, causes an amino acid change of arginine to histidine at codon 203 (p.(Arg203His)) of NM_000545.8. This variant segregated with diabetes, in more than 10 families with MODY (PP1_Strong; internal lab contributors). Additionally, this variant was identified in at least 15 unrelated individuals with non- autoimmune and non-absolute/near-absolute insulin-deficient diabetes (PS4; PMIDs: 23348805, 27913849, internal lab contributors). This variant resides in an amino acid within the HNF1α DNA binding domain that directly binds DNA, which is defined as critical for the protein’s function by the ClinGen MDEP (PM1) and is absent from gnomAD v2.1.1 (PM2_Supporting). This variant is also predicted to be deleterious by computational evidence, with a REVEL score of 0.958, which is greater than the MDEP VCEP threshold of 0.70 (PP3). Functional studies demonstrated the p.Arg203His protein has abnormal nuclear localization below 40% of wildtype, indicating that this variant impacts protein function (PMID: 32910913) (PS3_Supporting). Lastly, this variant was identified in an individual with a clinical history highly specific for HNF1A-MODY (MODY probability calculator result >50%, negative genetic testing for HNF4A, and antibody negative) (PP4_Moderate; PMID:27913849). In summary, c.608G>A meets the criteria to be classified as pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP (specification version 1.0, approved 9/30/21): PS4, PP1_Strong, PM1, PM2_Supporting, PP4_Moderate,PP3, PS3_Supporting. -

Diabetes mellitus type 1

Pathogenic:1

Likely pathogenic, no assertion criteria provided

clinical testing

Genetic Services Laboratory, University of Chicago

Aug 23, 2017

DNA sequence analysis of the HNF1A gene demonstrated a sequence change, c.608G>A, in exon 3 that results in an amino acid change, p.Arg203His. The p.Arg203His change affects a highly conserved amino acid residue located in a domain of the HNF1A protein that is known to be functional. The p.Arg203His substitution appears to be possibly damaging using several in-silico pathogenicity prediction tools (SIFT, PolyPhen2, REVEL). The p.Arg203His amino acid change has been described in the literature in one patient with early-onset diabetes (Ng et al., 1999. Diabet Med 16:956-63). In addition, different pathogenic sequence changes affecting the same amino acid residue (p.Arg203) has been described in patients with HNF1A-related maturity-onset diabetes of the young (MODY) (Lopez et al., 2011. Diabetes Res Clin Pract 91:208-12; Colclough et al., 2013. Hum Mutat 34:669-85; Yamada et al., 1999. Diabetes 48: 645-8). -

Maturity-onset diabetes of the young type 3

Pathogenic:1

Pathogenic, criteria provided, single submitter

research

Geisinger Clinic, Geisinger Health System

Aug 02, 2022

PS4, PP1_Strong, PM1, PM2, PP4_Moderate, PP3, PS3_Supporting -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

1.0

BayesDel_addAF

Pathogenic

0.43

BayesDel_noAF

Pathogenic

0.57

Cadd

Pathogenic

Dann

Pathogenic

1.0

Eigen

Pathogenic

0.70

Eigen_PC

Uncertain

0.62

FATHMM_MKL

Pathogenic

0.99

LIST_S2

Pathogenic

1.0

D;D;D;D;D

M_CAP

Pathogenic

0.89

MetaRNN

Pathogenic

0.98

D;D;D;D;D

MetaSVM

Pathogenic

1.1

MutationTaster

Benign

1.0

D;D;D;D;D

PrimateAI

Pathogenic

0.92

PROVEAN

Uncertain

-3.9

D;.;.;D;D

REVEL

Pathogenic

0.96

Sift

Uncertain

0.0010

D;.;.;D;D

Sift4G

Uncertain

0.0030

D;D;D;D;D

Polyphen

1.0

.;.;.;.;D

Vest4

0.96

MutPred

0.88

Gain of ubiquitination at K198 (P = 0.0371);Gain of ubiquitination at K198 (P = 0.0371);Gain of ubiquitination at K198 (P = 0.0371);Gain of ubiquitination at K198 (P = 0.0371);Gain of ubiquitination at K198 (P = 0.0371);

MVP

0.99

MPC

2.2

ClinPred

0.99

GERP RS

4.5

gMVP

0.98

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over