rs121912898
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM2PP2PP3_StrongPP5
The NM_001844.5(COL2A1):c.170G>A(p.Cys57Tyr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,736 control chromosomes in the GnomAD database, with no homozygous occurrence. 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).
Frequency
Consequence
NM_001844.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL2A1 | NM_001844.5 | c.170G>A | p.Cys57Tyr | missense_variant | 2/54 | ENST00000380518.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL2A1 | ENST00000380518.8 | c.170G>A | p.Cys57Tyr | missense_variant | 2/54 | 1 | NM_001844.5 | P1 | |
COL2A1 | ENST00000337299.7 | c.86-1610G>A | intron_variant | 1 | |||||
COL2A1 | ENST00000474996.6 | n.408G>A | non_coding_transcript_exon_variant | 3/8 | 3 | ||||
COL2A1 | ENST00000490609.2 | n.403G>A | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461736Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 727160
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Stickler syndrome, type I, nonsyndromic ocular Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jan 01, 2008 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at