rs1553738605
Positions:
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_198880.3(QRICH1):c.1953_1954insG(p.Arg652AlafsTer9) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Consequence
QRICH1
NM_198880.3 frameshift
NM_198880.3 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.512
Genes affected
QRICH1 (HGNC:24713): (glutamine rich 1) Enables DNA binding activity. Involved in several processes, including PERK-mediated unfolded protein response; intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress; and positive regulation of transcription, DNA-templated. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 12 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 3-49032715-G-GC is Pathogenic according to our data. Variant chr3-49032715-G-GC is described in ClinVar as [Pathogenic]. Clinvar id is 523658.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
QRICH1 | NM_198880.3 | c.1953_1954insG | p.Arg652AlafsTer9 | frameshift_variant | 8/10 | ENST00000395443.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
QRICH1 | ENST00000395443.7 | c.1953_1954insG | p.Arg652AlafsTer9 | frameshift_variant | 8/10 | 1 | NM_198880.3 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome Cov.: 31
GnomAD4 exome
Cov.:
31
GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Ververi-Brady syndrome Pathogenic:2
Pathogenic, criteria provided, single submitter | research | Institute of Human Genetics, University of Leipzig Medical Center | Dec 21, 2021 | - - |
Pathogenic, no assertion criteria provided | literature only | OMIM | May 15, 2018 | - - |
Computational scores
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Calibrated prediction
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Prediction
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at