rs587776795
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM4PP3PP5
The NM_006206.6(PDGFRA):c.1679_1693del(p.Arg560_Ser564del) variant causes a inframe deletion change involving the alteration of a conserved nucleotide. Variant has been reported in ClinVar as Pathogenic (no stars). Synonymous variant affecting the same amino acid position (i.e. R560R) has been classified as Likely benign.
Frequency
Genomes: not found (cov: 32)
Consequence
PDGFRA
NM_006206.6 inframe_deletion
NM_006206.6 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 9.91
Genes affected
PDGFRA (HGNC:8803): (platelet derived growth factor receptor alpha) This gene encodes a cell surface tyrosine kinase receptor for members of the platelet-derived growth factor family. These growth factors are mitogens for cells of mesenchymal origin. The identity of the growth factor bound to a receptor monomer determines whether the functional receptor is a homodimer or a heterodimer, composed of both platelet-derived growth factor receptor alpha and beta polypeptides. Studies suggest that this gene plays a role in organ development, wound healing, and tumor progression. Mutations in this gene have been associated with idiopathic hypereosinophilic syndrome, somatic and familial gastrointestinal stromal tumors, and a variety of other cancers. [provided by RefSeq, Mar 2012]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PM4
?
Nonframeshift variant in NON repetitive region in NM_006206.6.
PP3
?
No computational evidence supports a deleterious effect, but strongly conserved according to phyloP
PP5
?
Variant 4-54274864-GAGGGTCATTGAATCA-G is Pathogenic according to our data. Variant chr4-54274864-GAGGGTCATTGAATCA-G is described in ClinVar as [Pathogenic]. Clinvar id is 13548.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDGFRA | NM_006206.6 | c.1679_1693del | p.Arg560_Ser564del | inframe_deletion | 12/23 | ENST00000257290.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDGFRA | ENST00000257290.10 | c.1679_1693del | p.Arg560_Ser564del | inframe_deletion | 12/23 | 1 | NM_006206.6 | P1 | |
PDGFRA | ENST00000509092.5 | n.1497_1511del | non_coding_transcript_exon_variant | 11/15 | 1 | ||||
PDGFRA | ENST00000509490.5 | c.1679_1693del | p.Arg560_Ser564del | inframe_deletion, NMD_transcript_variant | 12/18 | 1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Gastrointestinal stromal tumor Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jan 31, 2003 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at