1-20633561-C-T
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_032409.3(PINK1):c.13C>T(p.Gln5*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000846 in 1,182,666 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★).
Frequency
Consequence
NM_032409.3 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151202Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000776 AC: 8AN: 1031464Hom.: 0 Cov.: 30 AF XY: 0.00000206 AC XY: 1AN XY: 486252
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151202Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 73826
ClinVar
Submissions by phenotype
Autosomal recessive early-onset Parkinson disease 6 Pathogenic:1
This sequence change creates a premature translational stop signal (p.Gln5*) in the PINK1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PINK1 are known to be pathogenic (PMID: 15087508, 15349870). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with PINK1-related conditions. ClinVar contains an entry for this variant (Variation ID: 661098). 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