5-134225824-C-T
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_002715.4(PPP2CA):c.38G>A(p.Trp13*) 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 Pathogenic (★).
Frequency
Consequence
NM_002715.4 stop_gained
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PPP2CA | NM_002715.4 | c.38G>A | p.Trp13* | stop_gained | Exon 1 of 7 | ENST00000481195.6 | NP_002706.1 | |
MIR3661 | NR_037434.1 | n.68C>T | non_coding_transcript_exon_variant | Exon 1 of 1 | ||||
MIR3661 | unassigned_transcript_863 | n.*26C>T | downstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PPP2CA | ENST00000481195.6 | c.38G>A | p.Trp13* | stop_gained | Exon 1 of 7 | 1 | NM_002715.4 | ENSP00000418447.1 | ||
ENSG00000272772 | ENST00000519718.2 | c.38G>A | p.Trp13* | stop_gained | Exon 1 of 6 | 5 | ENSP00000430774.2 | |||
ENSG00000273345 | ENST00000703317.1 | n.*73+17068G>A | intron_variant | Intron 4 of 9 | ENSP00000515260.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 31
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not provided Pathogenic:1
For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with PPP2CA-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Trp13*) in the PPP2CA gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PPP2CA are known to be pathogenic (PMID: 30595372). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.