rs587778595
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_006206.6(PDGFRA):c.1700_1701delCAinsGG(p.Pro567Arg) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. P567P) has been classified as Benign.
Frequency
Consequence
NM_006206.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PDGFRA | ENST00000257290.10 | c.1700_1701delCAinsGG | p.Pro567Arg | missense_variant | 1 | NM_006206.6 | ENSP00000257290.5 | |||
ENSG00000282278 | ENST00000507166.5 | c.1018-38_1018-37delCAinsGG | intron_variant | Intron 12 of 23 | 2 | ENSP00000423325.1 | ||||
PDGFRA | ENST00000509092.5 | n.1518_1519delCAinsGG | non_coding_transcript_exon_variant | Exon 11 of 15 | 1 | |||||
PDGFRA | ENST00000509490.5 | n.1700_1701delCAinsGG | non_coding_transcript_exon_variant | Exon 12 of 18 | 1 | ENSP00000424218.1 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
Gastrointestinal stromal tumor Uncertain:1
Information on the frequency of this variant in the gnomAD database is not available, as this variant may be reported differently in the database. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Not Available"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Not Available"). ClinVar contains an entry for this variant (Variation ID: 407423). This variant has not been reported in the literature in individuals affected with PDGFRA-related conditions. This sequence change replaces proline, which is neutral and non-polar, with arginine, which is basic and polar, at codon 567 of the PDGFRA protein (p.Pro567Arg). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at