rs1553747119
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PVS1PP5_Moderate
The NM_198880.3(QRICH1):c.138_139delinsTT(p.Gln46_Gln47delinsHisTer) variant causes a stop gained change involving the alteration of a conserved nucleotide. Variant has been reported in ClinVar as Pathogenic (★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 33)
Consequence
QRICH1
NM_198880.3 stop_gained
NM_198880.3 stop_gained
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 9.60
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 10 ACMG points.
PVS1
?
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PP5
?
Variant 3-49076879-GC-AA is Pathogenic according to our data. Variant chr3-49076879-GC-AA is described in ClinVar as [Pathogenic]. Clinvar id is 523659.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.138_139delinsTT | p.Gln46_Gln47delinsHisTer | stop_gained | 2/10 | ENST00000395443.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
QRICH1 | ENST00000395443.7 | c.138_139delinsTT | p.Gln46_Gln47delinsHisTer | stop_gained | 2/10 | 1 | NM_198880.3 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 genomes
?
Cov.:
33
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Cov.: 33
GnomAD4 genome
?
Cov.:
33
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Ververi-Brady syndrome Pathogenic:2
Pathogenic, no assertion criteria provided | literature only | OMIM | May 15, 2018 | - - |
Pathogenic, criteria provided, single submitter | research | Institute of Human Genetics, University of Leipzig Medical Center | Dec 21, 2021 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at