rs774573926
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The ENST00000460680.6(BAP1):c.358A>T(p.Lys120Ter) variant causes a stop gained 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 Likely pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. K120K) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
ENST00000460680.6 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BAP1 | NM_004656.4 | c.358A>T | p.Lys120Ter | stop_gained | 5/17 | ENST00000460680.6 | NP_004647.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BAP1 | ENST00000460680.6 | c.358A>T | p.Lys120Ter | stop_gained | 5/17 | 1 | NM_004656.4 | ENSP00000417132 | P1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome Cov.: 32
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not provided Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Aug 09, 2021 | DNA sequence analysis of the BAP1 gene demonstrated a sequence change, c.358A>T, in exon 5 that results in the creation of a premature stop codon at amino acid position 120, p.Lys120*. This sequence change is predicted to result in an abnormal transcript, which may be degraded, or may lead to the production of a truncated BAP1 protein with potentially abnormal function. Loss of function variants are known to be disease causing in the BAP1 gene. While this sequence change has not previously been described in the literature, other downstream truncating variants have been described in patients with cutaneous melanoma and mesothelioma (PMIDs: 30517737, 30975761). This sequence change is absent in the gnomAD population database. These collective evidences indicate that the p.Lys120* change is likely pathogenic, however functional studies have not been performed to prove this conclusively. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.