3-15478979-T-A
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PVS1PM2
The ENST00000383788.10(COLQ):c.391A>T(p.Lys131Ter) variant causes a stop gained, splice region change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
ENST00000383788.10 stop_gained, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COLQ | NM_005677.4 | c.391A>T | p.Lys131Ter | stop_gained, splice_region_variant | 5/17 | ENST00000383788.10 | NP_005668.2 | |
COLQ | NM_080538.2 | c.361A>T | p.Lys121Ter | stop_gained, splice_region_variant | 5/17 | NP_536799.1 | ||
COLQ | NM_080539.4 | c.289A>T | p.Lys97Ter | stop_gained, splice_region_variant | 4/16 | NP_536800.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COLQ | ENST00000383788.10 | c.391A>T | p.Lys131Ter | stop_gained, splice_region_variant | 5/17 | 1 | NM_005677.4 | ENSP00000373298 | P4 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 31
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at