rs121912882
Variant summary
Our verdict is Pathogenic. Variant got 17 ACMG points: 17P and 0B. PM1PM2PP2PP3_StrongPP5_Very_Strong
The NM_001844.5(COL2A1):c.2710C>T(p.Arg904Cys) variant causes a missense 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 (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R904H) has been classified as Likely benign.
Frequency
Consequence
NM_001844.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL2A1 | NM_001844.5 | c.2710C>T | p.Arg904Cys | missense_variant | 41/54 | ENST00000380518.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL2A1 | ENST00000380518.8 | c.2710C>T | p.Arg904Cys | missense_variant | 41/54 | 1 | NM_001844.5 | P1 | |
COL2A1 | ENST00000337299.7 | c.2503C>T | p.Arg835Cys | missense_variant | 40/53 | 1 | |||
COL2A1 | ENST00000493991.5 | n.1796C>T | non_coding_transcript_exon_variant | 24/37 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 30
GnomAD4 exome Cov.: 33
GnomAD4 genome ? Cov.: 30
ClinVar
Submissions by phenotype
not provided Pathogenic:6
Pathogenic, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Feb 07, 2020 | The COL2A1 c.2710C>T; p.Arg904Cys variant (rs121912882), also known in traditional nomenclature as Arg704Cys, is reported in the literature in multiple individuals and families affected with Stickler syndrome type I or a related skeletal dysplasia (Ballo 1998, Barat-Houari 2016, Goyal 2016, Guo 2017, Hoornaert 2006, Nagendran 2012, TomcÃkova 2018, Wang 2016, Yang 2018). In one family, the variant was observed to segregate with disease (Ballo 1998), while in another family the variant was found in the proband but neither parent, suggesting a de novo origin (Guo 2016). This variant is absent from general population databases (Exome Variant Server, Genome Aggregation Database), indicating it is not a common polymorphism. The arginine at codon 904 is highly conserved, it occurs in the collagen triple helix domain, and computational analyses (SIFT, PolyPhen-2) predict that this variant is deleterious. Arginine-to-cysteine substitutions in the COL2A1 triple helix domain have been reported in association with a spectrum of skeletal phenotypes and can interfere with collagen stability, trafficking, or fibril formation (Hoornaert 2006). Based on available information, the p.Arg904Cys variant is considered to be pathogenic. References: Ballo R et al. Stickler-like syndrome due to a dominant negative mutation in the COL2A1 gene. Am J Med Genet. 1998 Oct 30;80(1):6-11. Barat-Houari M et al. The expanding spectrum of COL2A1 gene variants IN 136 patients with a skeletal dysplasia phenotype. Eur J Hum Genet. 2016 Jul;24(7):992-1000. Goyal M et al. Stickler Syndrome Type 1 with Short Stature and Atypical Ocular Manifestations. Case Rep Pediatr. 2016;2016:3198597. Guo L et al. Novel and recurrent COL11A1 and COL2A1 mutations in the Marshall-Stickler syndrome spectrum. Hum Genome Var. 2017 Oct 5;4:17040. Hoornaert KP et al. The phenotypic spectrum in patients with arginine to cysteine mutations in the COL2A1 gene. J Med Genet. 2006 May;43(5):406-13. Nagendran S et al. Somatic mosaicism and the phenotypic expression of COL2A1 mutations. Am J Med Genet A. 2012 May;158A(5):1204-7. TomcÃkova D et al. Marshall and stickler syndrome in one family. Cesk Slov Oftalmol. Winter 2018;74(3):108-111. Wang X et al. Mutation survey and genotype-phenotype analysis of COL2A1 and COL11A1 genes in 16 Chinese patients with Stickler syndrome. Mol Vis. 2016 Jun 23;22:697-704. Yang L et al. Pathogenic gene screening in 91 Chinese patients with short stature of unknown etiology with a targeted next-generation sequencing panel. BMC Med Genet. 2018 Dec 12;19(1):212. - |
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Oct 26, 2023 | This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 904 of the COL2A1 protein (p.Arg904Cys). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with Stickler syndrome (PMID: 9800905, 22496037, 27390512, 28018693, 28983407). In at least one individual the variant was observed to be de novo. It has also been observed to segregate with disease in related individuals. This variant is also known as p.Arg704Cys. ClinVar contains an entry for this variant (Variation ID: 17379). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on COL2A1 protein function. For these reasons, this variant has been classified as Pathogenic. - |
Pathogenic, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Dec 08, 2022 | Occurs in the triple helical domain at the X position in the canonical Gly-X-Y repeat; other missense variants that introduce a cysteine residue in the triple helical domain have been reported in association with COL2A1-related disorders (HGMD); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 28018693, 22496037, 30541462, 20513134, 20179744, 26626311, 26443184, 28983407, 27390512, 16155195, 29453956, 30650974, 32427345, 32037395, 9800905) - |
Pathogenic, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Jun 22, 2017 | - - |
Multiple epiphyseal dysplasia, Beighton type Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Oct 30, 1998 | - - |
Myopia Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Centre for Mendelian Genomics, University Medical Centre Ljubljana | Jan 23, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at