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GeneBe

rs1553906632

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP2

The NM_006206.6(PDGFRA):​c.2947G>C​(p.Asp983His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D983Y) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 33)

Consequence

PDGFRA
NM_006206.6 missense

Scores

1
11
5

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 7.60
Variant links:
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 3 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP2
Missense variant where missense usually causes diseases, PDGFRA

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PDGFRANM_006206.6 linkuse as main transcriptc.2947G>C p.Asp983His missense_variant 22/23 ENST00000257290.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PDGFRAENST00000257290.10 linkuse as main transcriptc.2947G>C p.Asp983His missense_variant 22/231 NM_006206.6 P1P16234-1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.17
BayesDel_addAF
Uncertain
0.050
T
BayesDel_noAF
Benign
-0.17
CADD
Pathogenic
26
DANN
Uncertain
0.99
Eigen
Uncertain
0.57
Eigen_PC
Uncertain
0.57
FATHMM_MKL
Pathogenic
0.99
D
LIST_S2
Uncertain
0.87
D;D
M_CAP
Benign
0.062
D
MetaRNN
Uncertain
0.67
D;D
MetaSVM
Uncertain
-0.022
T
MutationTaster
Benign
0.95
D;D
PrimateAI
Uncertain
0.60
T
PROVEAN
Benign
-1.3
N;N
REVEL
Uncertain
0.39
Sift
Uncertain
0.0090
D;D
Sift4G
Uncertain
0.032
D;T
Polyphen
0.99
.;D
Vest4
0.56
MutPred
0.40
.;Gain of catalytic residue at R981 (P = 0.1457);
MVP
0.30
MPC
0.20
ClinPred
0.91
D
GERP RS
5.8
Varity_R
0.13
gMVP
0.62

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr4-55156546; API