rs387906558
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PM1PM2PM5PP2PP3_StrongPP5
The NM_001844.5(COL2A1):c.2149G>A(p.Gly717Ser) 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 Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G717V) has been classified as Likely pathogenic.
Frequency
Consequence
NM_001844.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL2A1 | NM_001844.5 | c.2149G>A | p.Gly717Ser | missense_variant | 33/54 | ENST00000380518.8 | |
LOC105369752 | XR_944910.2 | downstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL2A1 | ENST00000380518.8 | c.2149G>A | p.Gly717Ser | missense_variant | 33/54 | 1 | NM_001844.5 | P1 | |
COL2A1 | ENST00000337299.7 | c.1942G>A | p.Gly648Ser | missense_variant | 32/53 | 1 | |||
COL2A1 | ENST00000483376.1 | n.327G>A | non_coding_transcript_exon_variant | 4/8 | 5 | ||||
COL2A1 | ENST00000493991.5 | n.1073G>A | non_coding_transcript_exon_variant | 16/37 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome Cov.: 33
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Avascular necrosis of femoral head, primary, 1 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jun 02, 2005 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at