rs730882068
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_145239.3(PRRT2):c.516dupT(p.Glu173fs) variant causes a frameshift, stop gained change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_145239.3 frameshift, stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PRRT2 | ENST00000358758.12 | c.516dupT | p.Glu173fs | frameshift_variant, stop_gained | Exon 2 of 4 | 1 | NM_145239.3 | ENSP00000351608.7 | ||
ENSG00000280893 | ENST00000609618.2 | n.516dupT | non_coding_transcript_exon_variant | Exon 2 of 6 | 5 | ENSP00000476774.2 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome Cov.: 33
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
Episodic kinesigenic dyskinesia Pathogenic:1
This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Glu173*) in the PRRT2 gene. It is expected to result in an absent or disrupted protein product. This variant has been observed in individual(s) with PRRT2-related conditions (PMID: 22832103). It has also been observed to segregate with disease in related individuals. This variant is also known as c.516_517insT. ClinVar contains an entry for this variant (Variation ID: 31175). For these reasons, this variant has been classified as Pathogenic. Loss-of-function variants in PRRT2 are known to be pathogenic (PMID: 22623405, 22744660). -
Infantile convulsions and choreoathetosis Pathogenic:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at