rs121912832
Variant summary
Our verdict is Pathogenic. Variant got 15 ACMG points: 15P and 0B. PS1PM2PM5PP2PP3_StrongPP5_Moderate
The NM_000094.4(COL7A1):c.6007G>C(p.Gly2003Arg) variant causes a missense change. 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 nucleotide change resulting in the same amino acid substitution has been previously reported as Pathogenic in Lovd. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G2003E) has been classified as Pathogenic.
Frequency
Consequence
NM_000094.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 15 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COL7A1 | ENST00000681320.1 | c.6007G>C | p.Gly2003Arg | missense_variant | Exon 74 of 119 | NM_000094.4 | ENSP00000506558.1 | |||
COL7A1 | ENST00000328333.12 | c.6007G>C | p.Gly2003Arg | missense_variant | Exon 73 of 118 | 1 | ENSP00000332371.8 | |||
COL7A1 | ENST00000487017.5 | n.1924G>C | non_coding_transcript_exon_variant | Exon 39 of 83 | 5 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome Cov.: 39
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not provided Pathogenic:1
This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 2003 of the COL7A1 protein (p.Gly2003Arg). This variant is not present in population databases (gnomAD no frequency). A different variant (c.6007G>A) giving rise to the same protein effect has been determined to be pathogenic (PMID: 8752681). This suggests that this variant is also likely to be causative of disease. 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) performed at Invitae indicates that this missense variant is expected to disrupt COL7A1 protein function with a positive predictive value of 95%. This variant disrupts the triple helix domain of COL7A1. Glycine residues within the Gly-Xaa-Yaa repeats of the triple helix domain are required for the structure and stability of fibrillar collagens (PMID: 7695699, 8218237, 19344236), and variants at these glycine residues in COL7A1 are more frequently observed in individuals with disease than in the general population (PMID: 22058051). However, the clinical significance of this observation remains uncertain since only a limited number of affected individuals have been described to date. For these reasons, this variant has been classified as Pathogenic. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.