rs121912893
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_001844.5(COL2A1):c.1957C>T(p.Arg653Ter) 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 (★★). Synonymous variant affecting the same amino acid position (i.e. R653R) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_001844.5 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL2A1 | NM_001844.5 | c.1957C>T | p.Arg653Ter | stop_gained | 30/54 | ENST00000380518.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL2A1 | ENST00000380518.8 | c.1957C>T | p.Arg653Ter | stop_gained | 30/54 | 1 | NM_001844.5 | P1 | |
COL2A1 | ENST00000337299.7 | c.1750C>T | p.Arg584Ter | stop_gained | 29/53 | 1 | |||
COL2A1 | ENST00000483376.1 | n.135C>T | non_coding_transcript_exon_variant | 1/8 | 5 | ||||
COL2A1 | ENST00000493991.5 | n.881C>T | non_coding_transcript_exon_variant | 13/37 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1442782Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 715680
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not provided Pathogenic:3
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Dec 18, 2023 | This sequence change creates a premature translational stop signal (p.Arg653*) in the COL2A1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in COL2A1 are known to be pathogenic (PMID: 20179744). This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individuals with Stickler syndrome (PMID: 12544472). This variant is also known as p.R453X. ClinVar contains an entry for this variant (Variation ID: 17395). For these reasons, this variant has been classified as Pathogenic. - |
Pathogenic, criteria provided, single submitter | clinical testing | Blueprint Genetics | Nov 30, 2019 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Oct 22, 2021 | Reported in multiple individuals with Stickler syndrome referred for genetic testing at GeneDx and in published literature (Wilkin et al., 2000; Liberfarb et al., 2003; Richards et al., 2005; Hoornaert et al., 2010; Richards et al., 2010; Savasta et al., 2015); Estimated to account for 2% of molecularly confirmed cases of Stickler syndrome type 1 (Barat-Houari et al., 2016); Not observed in large population cohorts (gnomAD); 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; Reported in ClinVar as pathogenic (ClinVar Variant ID# 17395; ClinVar); Also known as R453*; This variant is associated with the following publications: (PMID: 20179744, 20301479, 20513134, 16752401, 10982970, 26443184, 12544472, 12939326, 24164106, 25809783, 29453956, 15671297, 26747767) - |
Stickler syndrome type 1 Pathogenic:2Other:1
Pathogenic, criteria provided, single submitter | clinical testing | Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center | Nov 10, 2023 | PVS1, PS4, PM2 - |
not provided, no classification provided | literature only | GeneReviews | - | - - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Sep 01, 2003 | - - |
Autosomal dominant rhegmatogenous retinal detachment Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Sep 01, 2003 | - - |
Legg-Calve-Perthes disease;C0220685:Achondrogenesis type II;C0265279:Kniest dysplasia;C0432214:Namaqualand hip dysplasia;C0796173:Spondyloperipheral dysplasia;C1835437:Platyspondylic dysplasia, Torrance type;C1836080:Stickler syndrome, type I, nonsyndromic ocular;C1836683:Spondyloepiphyseal dysplasia with metatarsal shortening;C1851536:Multiple epiphyseal dysplasia, Beighton type;C2020284:Stickler syndrome type 1;C2745959:Spondyloepiphyseal dysplasia congenita;C4225273:Spondyloepiphyseal dysplasia, Stanescu type;C4551562:Avascular necrosis of femoral head, primary, 1;C4759767:Spondylometaphyseal dysplasia Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 31, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at