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NM_006206.6(PDGFRA):c.1412A>G (p.Asn471Ser) AND Gastrointestinal stromal tumor

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Nov 27, 2023
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:
RCV001348838.7

Allele description [Variation Report for NM_006206.6(PDGFRA):c.1412A>G (p.Asn471Ser)]

NM_006206.6(PDGFRA):c.1412A>G (p.Asn471Ser)

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.1412A>G (p.Asn471Ser)
HGVS:
  • NC_000004.12:g.54273584A>G
  • NG_009250.1:g.49488A>G
  • NM_001347827.2:c.1412A>G
  • NM_001347828.2:c.1487A>G
  • NM_001347829.2:c.1412A>G
  • NM_001347830.2:c.1451A>G
  • NM_006206.4:c.1412A>G
  • NM_006206.6:c.1412A>GMANE SELECT
  • NP_001334756.1:p.Asn471Ser
  • NP_001334757.1:p.Asn496Ser
  • NP_001334758.1:p.Asn471Ser
  • NP_001334759.1:p.Asn484Ser
  • NP_006197.1:p.Asn471Ser
  • LRG_309t1:c.1412A>G
  • LRG_309:g.49488A>G
  • NC_000004.11:g.55139751A>G
Protein change:
N471S
Links:
dbSNP: rs1199380187
NCBI 1000 Genomes Browser:
rs1199380187
Molecular consequence:
  • NM_001347827.2:c.1412A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001347828.2:c.1487A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001347829.2:c.1412A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001347830.2:c.1451A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_006206.6:c.1412A>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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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001543156Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Nov 27, 2023) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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, SCV001543156.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This sequence change replaces asparagine, which is neutral and polar, with serine, which is neutral and polar, at codon 471 of the PDGFRA protein (p.Asn471Ser). This variant is present in population databases (no rsID available, gnomAD 0.007%). 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: 1044575). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. 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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 3, 2024