rs121908586
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2PP2PP3_Moderate
The NM_006206.6(PDGFRA):c.1682T>A(p.Val561Asp) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a damaging 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. V561A) has been classified as Uncertain significance.
Frequency
Consequence
NM_006206.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDGFRA | NM_006206.6 | c.1682T>A | p.Val561Asp | missense_variant | 12/23 | ENST00000257290.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDGFRA | ENST00000257290.10 | c.1682T>A | p.Val561Asp | missense_variant | 12/23 | 1 | NM_006206.6 | P1 | |
PDGFRA | ENST00000509092.5 | n.1500T>A | non_coding_transcript_exon_variant | 11/15 | 1 | ||||
PDGFRA | ENST00000509490.5 | c.1682T>A | p.Val561Asp | missense_variant, NMD_transcript_variant | 12/18 | 1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome Cov.: 31
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Gastrointestinal stromal tumor Pathogenic:2
Pathogenic, no assertion criteria provided | literature only | OMIM | Sep 01, 2007 | - - |
Pathogenic, no assertion criteria provided | literature only | Database of Curated Mutations (DoCM) | Jul 14, 2015 | - - |
Polyps, multiple and recurrent inflammatory fibroid, gastrointestinal Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Sep 01, 2007 | - - |
not provided Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing | Department of Pathology and Laboratory Medicine, Sinai Health System | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at