rs201486601
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 7P and 4B. PM1PP3_StrongPP5BS2
The NM_024411.5(PDYN):c.634C>T(p.Arg212Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000186 in 1,614,150 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 (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R212Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_024411.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDYN | NM_024411.5 | c.634C>T | p.Arg212Trp | missense_variant | 4/4 | ENST00000217305.3 | |
PDYN-AS1 | NR_134520.1 | n.1252+14111G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDYN | ENST00000217305.3 | c.634C>T | p.Arg212Trp | missense_variant | 4/4 | 1 | NM_024411.5 | P1 | |
PDYN-AS1 | ENST00000651021.1 | n.475+14111G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152156Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251408Hom.: 1 AF XY: 0.0000294 AC XY: 4AN XY: 135900
GnomAD4 exome AF: 0.0000178 AC: 26AN: 1461876Hom.: 0 Cov.: 31 AF XY: 0.0000179 AC XY: 13AN XY: 727238
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152274Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74460
ClinVar
Submissions by phenotype
Spinocerebellar ataxia type 23 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Nov 12, 2010 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at