NM_006206.6(PDGFRA):c.3179T>A (p.Ile1060Asn) AND Polyps, multiple and recurrent inflammatory fibroid, gastrointestinal

Germline classification:: Uncertain significance (3 submissions)
Last evaluated:: Oct 31, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV001535433.4

Allele description [Variation Report for NM_006206.6(PDGFRA):c.3179T>A (p.Ile1060Asn)]

NM_006206.6(PDGFRA):c.3179T>A (p.Ile1060Asn)

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.3179T>A (p.Ile1060Asn)

HGVS:

NC_000004.12:g.54295181T>A
NG_009250.1:g.71085T>A
NM_001347828.2:c.3254T>A
NM_001347829.2:c.3179T>A
NM_001347830.2:c.3218T>A
NM_006206.6:c.3179T>AMANE SELECT
NP_001334757.1:p.Ile1085Asn
NP_001334758.1:p.Ile1060Asn
NP_001334759.1:p.Ile1073Asn
NP_006197.1:p.Ile1060Asn
LRG_309t1:c.3179T>A
LRG_309:g.71085T>A
NC_000004.11:g.55161348T>A
NM_006206.4:c.3179T>A
NM_006206.5:c.3179T>A

Protein change:

I1060N

Links:

dbSNP: rs774522904

NCBI 1000 Genomes Browser:

rs774522904

Molecular consequence:

NM_001347828.2:c.3254T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001347829.2:c.3179T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001347830.2:c.3218T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_006206.6:c.3179T>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Polyps, multiple and recurrent inflammatory fibroid, gastrointestinal
Identifiers:: MONDO: MONDO:0008285; MedGen: C5193005; OMIM: 175510

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001749324	GenomeConnect - Invitae Patient Insights Network	no classification provided	not provided	unknown	phenotyping only
SCV002584622	St. Jude Molecular Pathology, St. Jude Children's Research Hospital	criteria provided, single submitter (St. Jude Assertion Criteria 2020)	Uncertain significance (Sep 8, 2022)	germline	clinical testing	Citation Link,
SCV004200884	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Oct 31, 2023)	unknown	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

SCV001749324

GenomeConnect - Invitae Patient Insights Network

no classification provided

not provided

unknown

phenotyping only

SCV002584622

St. Jude Molecular Pathology, St. Jude Children's Research Hospital

criteria provided, single submitter

(St. Jude Assertion Criteria 2020)

Uncertain significance
(Sep 8, 2022)

germline

clinical testing

Citation Link,

SCV004200884

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Oct 31, 2023)

unknown

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
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing, phenotyping only

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From GenomeConnect - Invitae Patient Insights Network, SCV001749324.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	phenotyping only	not provided

Description

Variant interpreted as Uncertain significance and reported on 09-29-2017 by Invitae. GenomeConnect-Invitae Patient Insights Network assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. Registry team members make no attempt to reinterpret the clinical significance of the variant. Phenotypic details are available under supporting information.

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

From St. Jude Molecular Pathology, St. Jude Children's Research Hospital, SCV002584622.1

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

Description

The PDGFRA c.3179T>A (p.Ile1060Asn) missense change has a maximum subpopulation frequency of 0.0093% in gnomAD v2.1.1 (https://gnomad.broadinstitute.org/). The in silico tool REVEL predicts a benign effect on protein function, but to our knowledge this prediction has not been confirmed by functional studies. To our knowledge, this variant has not been reported in individuals with PDGFRA-associated tumors. In summary, the evidence currently available is insufficient to determine the clinical significance of this variant. It has therefore been classified as 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

From Baylor Genetics, SCV004200884.1

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

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

Last Updated: May 12, 2024

ClinVar

Relating variation to medicine