rs1553508338
Variant summary
Our verdict is Pathogenic. Variant got 19 ACMG points: 19P and 0B. PM1PM2PM5PP2PP3_StrongPP5_Very_Strong
The ENST00000304636.9(COL3A1):c.1762G>A(p.Gly588Ser) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,758 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 14/23 in silico tools predict a damaging outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. 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. G588D) has been classified as Likely pathogenic.
Frequency
Consequence
ENST00000304636.9 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COL3A1 | NM_000090.4 | c.1762G>A | p.Gly588Ser | missense_variant, splice_region_variant | 25/51 | ENST00000304636.9 | NP_000081.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COL3A1 | ENST00000304636.9 | c.1762G>A | p.Gly588Ser | missense_variant, splice_region_variant | 25/51 | 1 | NM_000090.4 | ENSP00000304408 | P1 | |
COL3A1 | ENST00000450867.2 | c.1663G>A | p.Gly555Ser | missense_variant, splice_region_variant | 24/50 | 1 | ENSP00000415346 |
Frequencies
GnomAD3 genomes Cov.: 30
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461758Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 727188
GnomAD4 genome Cov.: 30
ClinVar
Submissions by phenotype
Familial thoracic aortic aneurysm and aortic dissection Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 10, 2021 | The p.G588S pathogenic mutation (also known as c.1762G>A) is located in coding exon 25 of the COL3A1 gene. The glycine at codon 588 is replaced by serine, an amino acid with similar properties. This change occurs in the first base pair of coding exon 25. The majority (approximately two-thirds) of COL3A1 mutations identified to date have involved the substitution of another amino acid for glycine within the triple-helical domain. Internal structural analysis indicates that this alteration disrupts the characteristic G-X-Y motif in the COL3A1 protein and inserts a bulky side chain into a sterically-constrained region (Bella J et al. Science. 1994;266:75-81; Hohenester E et al. Proc. Natl. Acad. Sci. U.S.A. 2008;105:18273-7; Ambry internal data). Two alterations in the same codon, p.G588D and p.G588V, have also been reported in individuals with vascular Ehlers-Danlos syndrome (EDS) (Pepin M et al. N. Engl. J. Med. 2000 Mar; 342(10):673-80; Pepin MG et al. Genet. Med. 2014 Dec; 16(12):881-8; Frank M et al. Eur. J. Hum. Genet. 2015 Dec; 23(12):1657-64). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. - |
Ehlers-Danlos syndrome, type 4 Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Nov 28, 2016 | Variant summary: The COL3A1 c.1762G>A (p.Gly588Ser) variant involves the alteration of a conserved nucleotide located in the first position of exon 25. 5/5 in silico tools predict a damaging outcome for this variant. 2/5 splice prediction tools predict the variant to result in weaking of the a canonical splice acceptor site. However, these predictions have yet to be confirmed by functional studies. This variant is absent in 121398 control chromosomes. The variant of interest has not, to our knowledge, been reported in affected individuals via publications and/or reputable databases/clinical diagnostic laboratories; nor evaluated for functional impact by in vivo/vitro studies. However, the majority of identified pathogenic variants in COL3A1 result in substitution of other amino acids for glycine residues in the Gly-X-Y triplets of the major helical domain where this variant is located. Therefore, this variant has been classified as likely pathogenic. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at