rs587779715
Variant summary
Our verdict is Pathogenic. Variant got 19 ACMG points: 19P and 0B. PM1PM2PM5PP2PP3_StrongPP5_Very_Strong
The NM_000090.4(COL3A1):c.3472G>C(p.Gly1158Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G1158D) has been classified as Pathogenic.
Frequency
Consequence
NM_000090.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Pathogenic. Variant got 19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL3A1 | NM_000090.4 | c.3472G>C | p.Gly1158Arg | missense_variant | 47/51 | ENST00000304636.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL3A1 | ENST00000304636.9 | c.3472G>C | p.Gly1158Arg | missense_variant | 47/51 | 1 | NM_000090.4 | P1 | |
COL3A1 | ENST00000450867.2 | c.3373G>C | p.Gly1125Arg | missense_variant | 46/50 | 1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Cov.: 31
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Loeys-Dietz syndrome Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Molecular Diagnostic Laboratory for Inherited Cardiovascular Disease, Montreal Heart Institute | Sep 22, 2016 | - - |
COL3A1-related disorder Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 14, 2022 | The COL3A1 c.3472G>C variant is predicted to result in the amino acid substitution p.Gly1158Arg. This variant was reported in a study of individuals with vascular Ehlers-Danlos syndrome (EDS type IV) (Supplementary Table S1, Pepin et al. 2014. PubMed ID: 24922459). Of note, another variant impacting this same amino acid was also reported in the same study of individuals with vascular EDS [c.3473G>A (p.Gly1158Asp), Supplementary Table S1, Pepin et al. 2014. PubMed ID: 24922459]. The c.3472G>C variant has not been reported in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. The majority of documented causative missense variants in COL3A1 substitute a glycine residue to another amino acid in the Gly-X-Y triple helical domain (Pepin et al. 2014. PubMed ID: 24922459). Taken together, we interpret this variant as likely pathogenic. - |
Ehlers-Danlos syndrome, type 4 Pathogenic:1
Pathogenic, no assertion criteria provided | clinical testing | Collagen Diagnostic Laboratory, University of Washington | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at