6-165333065-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 3P and 2B. PM2PP2BP4_Moderate
The NM_001385079.1(PDE10A):c.3128C>A(p.Ser1043Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001385079.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PDE10A | NM_001385079.1 | c.3128C>A | p.Ser1043Tyr | missense_variant | 22/22 | ENST00000539869.4 | NP_001372008.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PDE10A | ENST00000539869.4 | c.3128C>A | p.Ser1043Tyr | missense_variant | 22/22 | 1 | NM_001385079.1 | ENSP00000438284 | P3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 30
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Infantile-onset generalized dyskinesia with orofacial involvement Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | New York Genome Center | Oct 30, 2020 | The c.2300C>A; (p.Ser767Tyr) missense variant in exon 23 of 23 of PDE10A has not been reported in affected individuals in the available literature. This variant is absent in gnomADv3 indicating it is not a common benign variant in the populations represented in this database. In silico predictors suggest this variant is Benign (REVEL; score: 0.082) and Damaging (SIFT; score: 0.015). Given the evidence regarding its pathogenicity, the c.2300C>A; (p.Ser767Tyr) variant identified in the PDE10A gene is reported as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.