rs397515511
Variant summary
Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PS1_Very_StrongPM2PP3_Strong
The ENST00000222271.7(COMP):c.1665C>A(p.Asn555Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. 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 not provided (no stars). Another nucleotide change resulting in same amino acid change has been previously reported as Likely pathogenicin ClinVar.
Frequency
Consequence
ENST00000222271.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COMP | NM_000095.3 | c.1665C>A | p.Asn555Lys | missense_variant | 14/19 | ENST00000222271.7 | NP_000086.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COMP | ENST00000222271.7 | c.1665C>A | p.Asn555Lys | missense_variant | 14/19 | 1 | NM_000095.3 | ENSP00000222271 | P1 | |
COMP | ENST00000542601.6 | c.1566C>A | p.Asn522Lys | missense_variant | 13/18 | 1 | ENSP00000439156 | |||
COMP | ENST00000425807.1 | c.1506C>A | p.Asn502Lys | missense_variant | 13/18 | 2 | ENSP00000403792 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 35
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Multiple epiphyseal dysplasia Other:1
not provided, no classification provided | literature only | GeneReviews | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at