2-218339847-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4BP6
The NM_015488.5(PNKD):c.301C>T(p.Arg101Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000273 in 1,613,174 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R101Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_015488.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PNKD | NM_015488.5 | c.301C>T | p.Arg101Trp | missense_variant | 3/10 | ENST00000273077.9 | |
CATIP-AS2 | NR_125777.1 | n.120+11313G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PNKD | ENST00000273077.9 | c.301C>T | p.Arg101Trp | missense_variant | 3/10 | 1 | NM_015488.5 | ||
CATIP-AS2 | ENST00000411433.1 | n.120+11313G>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000527 AC: 8AN: 151942Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000129 AC: 32AN: 249008Hom.: 0 AF XY: 0.000119 AC XY: 16AN XY: 134798
GnomAD4 exome AF: 0.0000246 AC: 36AN: 1461114Hom.: 0 Cov.: 32 AF XY: 0.0000179 AC XY: 13AN XY: 726810
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152060Hom.: 0 Cov.: 31 AF XY: 0.0000134 AC XY: 1AN XY: 74350
ClinVar
Submissions by phenotype
Paroxysmal nonkinesigenic dyskinesia 1 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Oct 03, 2019 | - - |
Paroxysmal nonkinesigenic dyskinesia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 27, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at