rs796052941
Variant summary
Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PVS1_StrongPM2PP5_Very_Strong
The NM_145239.3(PRRT2):c.971del(p.Gly324GlufsTer13) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000187 in 1,608,246 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely pathogenic (★★). Synonymous variant affecting the same amino acid position (i.e. V322V) has been classified as Likely benign.
Frequency
Consequence
NM_145239.3 frameshift
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 | UniProt |
---|---|---|---|---|---|---|---|
PRRT2 | NM_145239.3 | c.971del | p.Gly324GlufsTer13 | frameshift_variant | 3/4 | ENST00000358758.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRRT2 | ENST00000358758.12 | c.971del | p.Gly324GlufsTer13 | frameshift_variant | 3/4 | 1 | NM_145239.3 | P1 | |
MVP-DT | ENST00000569039.5 | n.246-4246del | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 152064Hom.: 0 Cov.: 32
GnomAD4 exome AF: 6.87e-7 AC: 1AN: 1456182Hom.: 0 Cov.: 35 AF XY: 0.00000138 AC XY: 1AN XY: 724294
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 152064Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74272
ClinVar
Submissions by phenotype
not provided Pathogenic:2
Likely pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Nov 06, 2015 | The c.971delG variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. It was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The c.971delG variant causes a frameshift starting with codon Glycine 324, changes this amino acid to a Glutamic acid residue and creates a premature Stop codon at position 13 of the new reading frame, denoted p.Gly324GlufsX13. This variant is predicted to cause loss of normal protein function through protein truncation as the last 17 amino acids of the PRRT2 protein are lost and replaced by 12 incorrect amino acids. Although this variant has not been previously reported to our knowledge, other frameshift variants have been reported in the Human Gene Mutation Database in association with PRRT2-related disorders (Stenson et al., 2014). - |
Likely pathogenic, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2023 | PRRT2: PM2, PS4:Moderate, PVS1:Moderate, PP4 - |
Episodic kinesigenic dyskinesia 1 Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Mendelics | May 04, 2022 | - - |
Seizures, benign familial infantile, 2 Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Neuberg Centre For Genomic Medicine, NCGM | - | The frameshift deletion p.G324Efs*13 in PRRT2 (NM_145239.2) has been observed before in a patient with paroxysmal kinesigenic dyskinesia (Liu YT et al). It has been submitted to ClinVar as Likely Pathogenic. Other missense variants occuring at this residue have been deemed to be disease causing (Tsai MH et al). The p.G324Efs*13 variant is novel not in any individuals) in gnomAD Exomes and is novel (not in any individuals) in 1000 Genomes. This variant is predicted to cause loss of normal protein function through protein truncation caused a frameshift mutation. The frame shifted sequence continues 13 residues until a stop codon is reached. For these reasons, this variant has been classified as Pathogenic. - |
Episodic kinesigenic dyskinesia Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Oct 17, 2023 | This sequence change creates a premature translational stop signal (p.Gly324Glufs*13) in the PRRT2 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 17 amino acid(s) of the PRRT2 protein. This variant is present in population databases (rs796052941, gnomAD 0.01%). This premature translational stop signal has been observed in individual(s) with PRRT2-related conditions (PMID: 30386286). ClinVar contains an entry for this variant (Variation ID: 206696). This variant disrupts a region of the PRRT2 protein in which other variant(s) (p.Ile327Met) have been determined to be pathogenic (PMID: 2131349, 23496026, 24609974, 24886244). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at