rs587778399
Variant summary
Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PVS1_StrongPM2PP5_Very_Strong
The NM_000545.8(HNF1A):c.1720_1733delinsGGCATCCAGCACC(p.Ser574GlyfsTer86) variant causes a frameshift change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely pathogenic (★★★).
Frequency
Genomes: not found (cov: 32)
Consequence
HNF1A
NM_000545.8 frameshift
NM_000545.8 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 5.45
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 14 ACMG points.
PVS1
?
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most 50 bp of the penultimate exon, not predicted to undergo nonsense mediated mRNA decay. There are 18 pathogenic variants in the truncated region.
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant 12-120999579-AGCATCCAGCACCT-GGCATCCAGCACC is Pathogenic according to our data. Variant chr12-120999579-AGCATCCAGCACCT-GGCATCCAGCACC is described in ClinVar as [Likely_pathogenic]. Clinvar id is 1687089.Status of the report is reviewed_by_expert_panel, 3 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HNF1A | NM_000545.8 | c.1720_1733delinsGGCATCCAGCACC | p.Ser574GlyfsTer86 | frameshift_variant | 9/10 | ENST00000257555.11 | |
HNF1A | NM_001306179.2 | c.1741_1754delinsGGCATCCAGCACC | p.Ser581GlyfsTer86 | frameshift_variant | 9/10 | ||
HNF1A | NM_001406915.1 | c.1528_1541delinsGGCATCCAGCACC | p.Ser510GlyfsTer86 | frameshift_variant | 8/9 | ||
HNF1A | XM_024449168.2 | c.1813_1826delinsGGCATCCAGCACC | p.Ser605GlyfsTer86 | frameshift_variant | 8/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HNF1A | ENST00000257555.11 | c.1720_1733delinsGGCATCCAGCACC | p.Ser574GlyfsTer86 | frameshift_variant | 9/10 | 1 | NM_000545.8 | P4 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Likely pathogenic
Submissions summary: Pathogenic:1
Revision: reviewed by expert panel
LINK: link
Submissions by phenotype
Monogenic diabetes Pathogenic:1
Likely pathogenic, reviewed by expert panel | curation | ClinGen Monogenic Diabetes Variant Curation Expert Panel | Apr 17, 2022 | The c.1720_1733del variant in the HNF1 homeobox A gene, HNF1A, causes a frameshift in the protein at codon 578 (NM_000545.8), adding 82 novel amino acids before encountering a stop codon (p.(Leu578ArgfsTer82)). While this variant, located in exon 9 of 10, is predicted to cause a premature stop codon in a position that escapes nonsense mediated decay, it results in the loss of a functionally important region of a gene where loss-of-function is an established disease mechanism (PVS1; PMID: 23348805). Additionally, this variant is absent from gnomAD v2.1.1 (PM2_Supporting). In summary, c.1733del 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. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at