rs1555211999

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong

The NM_000545.8(HNF1A):​c.790_791del​(p.Val264LeufsTer52) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely pathogenic (★★★). Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: not found (cov: 32)

Consequence

HNF1A
NM_000545.8 frameshift

Scores

Not classified

Clinical Significance

Likely pathogenic reviewed by expert panel P:2O:1

Conservation

PhyloP100: 9.50
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]

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ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 18 ACMG points.

PVS1
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 12-120994237-CGT-C is Pathogenic according to our data. Variant chr12-120994237-CGT-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 447500.Status of the report is reviewed_by_expert_panel, 3 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
HNF1ANM_000545.8 linkuse as main transcriptc.790_791del p.Val264LeufsTer52 frameshift_variant 4/10 ENST00000257555.11
HNF1ANM_001306179.2 linkuse as main transcriptc.790_791del p.Val264LeufsTer52 frameshift_variant 4/10
HNF1ANM_001406915.1 linkuse as main transcriptc.790_791del p.Val264LeufsTer52 frameshift_variant 4/9
HNF1AXM_024449168.2 linkuse as main transcriptc.790_791del p.Val264LeufsTer52 frameshift_variant 4/9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
HNF1AENST00000257555.11 linkuse as main transcriptc.790_791del p.Val264LeufsTer52 frameshift_variant 4/101 NM_000545.8 P4

Frequencies

GnomAD3 genomes
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Cov.:
32

ClinVar

Significance: Likely pathogenic
Submissions summary: Pathogenic:2Other:1
Revision: reviewed by expert panel
LINK: link

Submissions by phenotype

Monogenic diabetes Pathogenic:1
Likely pathogenic, reviewed by expert panelcurationClinGen Monogenic Diabetes Variant Curation Expert PanelApr 18, 2022The c.790_791del variant in the HNF1 homeobox A gene, HNF1A, causes a frameshift in the protein at codon 264 of NM_000545.8, adding 52 novel amino acids before encountering a stop codon (p.(Val264LeufsTer52)). This variant, located in biologically-relevant exon 4 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). Additionally, this variant is absent from gnomAD v2.1.1 (PM2_Supporting). This variant was identified in two unrelated individuals with non-autoimmune and non-absolute/near-absolute insulin-deficient diabetes; however, PS4_Moderate cannot be applied because this number is below the ClinGen MDEP threshold (PMID: 31365591, internal lab contributors). Neither of these individuals had a calculated MODY probability score >= 50%; therefore PP4 cannot be applied. In summary, c.790_791del meets the criteria to be classified as likely pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP (specification version 1.1, approved 9/30/21): PVS1, PM2_Supporting. -
not provided Pathogenic:1
Pathogenic, criteria provided, single submitterclinical testingAthena DiagnosticsJun 26, 2017- -
Maturity onset diabetes mellitus in young Other:1
Uncertain risk allele, criteria provided, single submitterresearchClinical 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. However, more evidence is required to confer the association of this particular variant rs1555211999 with MODY3. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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.

Other links and lift over

dbSNP: rs1555211999; hg19: chr12-121432040; API