NM_006206.6(PDGFRA):c.1274A>G (p.His425Arg) AND Gastrointestinal stromal tumor

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Feb 1, 2024
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000463210.12

Allele description [Variation Report for NM_006206.6(PDGFRA):c.1274A>G (p.His425Arg)]

NM_006206.6(PDGFRA):c.1274A>G (p.His425Arg)

Gene:

PDGFRA:platelet derived growth factor receptor alpha [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

4q12

Genomic location:

Preferred name:

NM_006206.6(PDGFRA):c.1274A>G (p.His425Arg)

HGVS:

NC_000004.12:g.54272430A>G
NG_009250.1:g.48334A>G
NM_001347827.2:c.1274A>G
NM_001347828.2:c.1349A>G
NM_001347829.2:c.1274A>G
NM_001347830.2:c.1313A>G
NM_006206.6:c.1274A>GMANE SELECT
NP_001334756.1:p.His425Arg
NP_001334757.1:p.His450Arg
NP_001334758.1:p.His425Arg
NP_001334759.1:p.His438Arg
NP_006197.1:p.His425Arg
LRG_309t1:c.1274A>G
LRG_309:g.48334A>G
NC_000004.11:g.55138597A>G
NM_006206.4:c.1274A>G
NM_006206.5:c.1274A>G

Protein change:

H425R

Links:

dbSNP: rs769631321

NCBI 1000 Genomes Browser:

rs769631321

Molecular consequence:

NM_001347827.2:c.1274A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001347828.2:c.1349A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001347829.2:c.1274A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001347830.2:c.1313A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_006206.6:c.1274A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Gastrointestinal stromal tumor
Synonyms:: Gastrointestinal Stromal Sarcoma; Gastrointestinal stromal tumor, somatic; Gastrointestinal stroma tumor
Identifiers:: MONDO: MONDO:0011719; MeSH: D046152; MedGen: C0238198; Orphanet: 44890; OMIM: 606764; Human Phenotype Ontology: HP:0100723

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000546608	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Feb 1, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000546608

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Feb 1, 2024)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group, Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000546608.9

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

This sequence change replaces histidine, which is basic and polar, with arginine, which is basic and polar, at codon 425 of the PDGFRA protein (p.His425Arg). This variant is present in population databases (rs769631321, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with PDGFRA-related conditions. ClinVar contains an entry for this variant (Variation ID: 407410). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt PDGFRA protein function with a negative predictive value of 80%. 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.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 13, 2024

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