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NM_002834.5(PTPN11):c.1507G>C (p.Gly503Arg) AND PTPN11-related disorder

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Apr 30, 2024
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV004532494.2

Allele description [Variation Report for NM_002834.5(PTPN11):c.1507G>C (p.Gly503Arg)]

NM_002834.5(PTPN11):c.1507G>C (p.Gly503Arg)

Gene:
PTPN11:protein tyrosine phosphatase non-receptor type 11 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
12q24.13
Genomic location:
Preferred name:
NM_002834.5(PTPN11):c.1507G>C (p.Gly503Arg)
Other names:
p.G503R:GGG>CGG
HGVS:
  • NC_000012.12:g.112489083G>C
  • NG_007459.1:g.75352G>C
  • NM_001330437.2:c.1519G>C
  • NM_001374625.1:c.1504G>C
  • NM_002834.5:c.1507G>CMANE SELECT
  • NP_001317366.1:p.Gly507Arg
  • NP_001361554.1:p.Gly502Arg
  • NP_002825.3:p.Gly503Arg
  • NP_002825.3:p.Gly503Arg
  • LRG_614t1:c.1507G>C
  • LRG_614:g.75352G>C
  • NC_000012.11:g.112926887G>C
  • NM_001330437.1:c.1519G>C
  • NM_002834.3:c.1507G>C
  • NM_002834.4:c.1507G>C
Protein change:
G502R
Links:
dbSNP: rs397507545
NCBI 1000 Genomes Browser:
rs397507545
Molecular consequence:
  • NM_001330437.2:c.1519G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374625.1:c.1504G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_002834.5:c.1507G>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
PTPN11-related disorder
Identifiers:

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004118266PreventionGenetics, part of Exact Sciences
no assertion criteria provided
Pathogenic
(Apr 30, 2024) 		germlineclinical testing

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV004118266.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The PTPN11 c.1507G>C variant is predicted to result in the amino acid substitution p.Gly503Arg. This variant is located in a mutational hotspot region of the PTPN11 gene. It has been repeatedly reported to be causative for Noonan syndrome (Sarkozy et al. 2003. PubMed ID: 12960218; Holmfeldt et al. 2013. PubMed ID: 23334668; Chinton et al. 2019. PubMed ID: 31560489). Additionally, a different variant, 1507G>A, that results in the same amino acid change has been reported as causative for Noonan syndrome (Tartaglia et al. 2006. PubMed ID: 16358218). At PreventionGenetics, we previously detected the variant c.1507G>C in other affected patients. This variant is reported in 0.0046% of alleles in individuals of European (Finnish) descent in gnomAD. This variant is interpreted as pathogenic.

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

Last Updated: Oct 13, 2024