3-49032715-G-A
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_198880.3(QRICH1):c.1954C>T(p.Arg652Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
QRICH1
NM_198880.3 stop_gained
NM_198880.3 stop_gained
Scores
3
3
1
Clinical Significance
Conservation
PhyloP100: 3.05
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 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 3-49032715-G-A is Pathogenic according to our data. Variant chr3-49032715-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 523657.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-49032715-G-A is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
QRICH1 | NM_198880.3 | c.1954C>T | p.Arg652Ter | stop_gained | 8/10 | ENST00000395443.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
QRICH1 | ENST00000395443.7 | c.1954C>T | p.Arg652Ter | stop_gained | 8/10 | 1 | NM_198880.3 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1459096Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 725904
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1459096
Hom.:
Cov.:
31
AF XY:
AC XY:
0
AN XY:
725904
Gnomad4 AFR exome
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Gnomad4 FIN exome
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Gnomad4 OTH exome
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GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:4
Revision: criteria provided, multiple submitters, no conflicts
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 | Jun 04, 2021 | - - |
not provided Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Jan 20, 2021 | Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 28692176, 33009816, 28135719, 28191890, 31785789) - |
Intellectual disability Pathogenic:1
Pathogenic, criteria provided, single submitter | research | Institute of Human Genetics, University of Leipzig Medical Center | Jun 05, 2020 | The stop variant c.1954C>T, p.(Arg652*) in QRICH1 was identified by trio exome sequencing in a boy with global developmental delay, muscular hypotonia, microcephaly, neurodermitis and obstipation. This variant has not been reported in the general population and but has been described as a disease causing previously (PMID: 28692176). The healthy and unrelated parents did not carry the variant, confirming de novo status. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
Cadd
Pathogenic
Dann
Uncertain
Eigen
Pathogenic
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
MutationTaster
Benign
A;A;A
Vest4
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at