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NM_002834.5(PTPN11):c.178G>A (p.Gly60Ser) AND PTPN11-related disorder

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jul 3, 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:
RCV004532484.1

Allele description [Variation Report for NM_002834.5(PTPN11):c.178G>A (p.Gly60Ser)]

NM_002834.5(PTPN11):c.178G>A (p.Gly60Ser)

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.178G>A (p.Gly60Ser)
Other names:
p.G60S:GGT>AGT
HGVS:
  • NC_000012.12:g.112450358G>A
  • NG_007459.1:g.36627G>A
  • NM_001330437.2:c.178G>A
  • NM_001374625.1:c.175G>A
  • NM_002834.5:c.178G>AMANE SELECT
  • NM_080601.3:c.178G>A
  • NP_001317366.1:p.Gly60Ser
  • NP_001361554.1:p.Gly59Ser
  • NP_002825.3:p.Gly60Ser
  • NP_542168.1:p.Gly60Ser
  • LRG_614t1:c.178G>A
  • LRG_614:g.36627G>A
  • NC_000012.11:g.112888162G>A
  • NM_002834.3:c.178G>A
  • NM_002834.4:c.178G>A
  • NM_002834.5:c.178G>A
Protein change:
G59S
Links:
dbSNP: rs397507507
NCBI 1000 Genomes Browser:
rs397507507
Molecular consequence:
  • NM_001330437.2:c.178G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374625.1:c.175G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_002834.5:c.178G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_080601.3:c.178G>A - 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
SCV004118948PreventionGenetics, part of Exact Sciences
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Jul 3, 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

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 PreventionGenetics, part of Exact Sciences, SCV004118948.1

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

Description

The PTPN11 c.178G>A variant is predicted to result in the amino acid substitution p.Gly60Ser. This variant has been reported in individuals with Noonan syndrome/RASopathy phenotypes, with at least one case confirmed to have occurred de novo (Ezquieta et al. 2012. PubMed ID: 22465605; Bertelloni et al. 2013. PubMed ID: 23624134). This variant has not been reported in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. Different amino acid substitutions affecting the same amino acid (p.Gly60Cys, p.Gly60Ala, p.Gly60Val) have been reported in individuals with Noonan syndrome (Human Gene Mutation Database). The c.178G>A (p.Gly60Ser) variant is interpreted as pathogenic.

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

Last Updated: Nov 3, 2024