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NM_002834.5(PTPN11):c.1502G>A (p.Arg501Lys) AND Noonan syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jan 26, 2016
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:
RCV000037618.14

Allele description [Variation Report for NM_002834.5(PTPN11):c.1502G>A (p.Arg501Lys)]

NM_002834.5(PTPN11):c.1502G>A (p.Arg501Lys)

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.1502G>A (p.Arg501Lys)
Other names:
p.R501K:AGG>AAG
HGVS:
  • NC_000012.12:g.112489078G>A
  • NG_007459.1:g.75347G>A
  • NM_001330437.2:c.1514G>A
  • NM_001374625.1:c.1499G>A
  • NM_002834.5:c.1502G>AMANE SELECT
  • NP_001317366.1:p.Arg505Lys
  • NP_001361554.1:p.Arg500Lys
  • NP_002825.3:p.Arg501Lys
  • NP_002825.3:p.Arg501Lys
  • LRG_614t1:c.1502G>A
  • LRG_614:g.75347G>A
  • LRG_614p1:p.Arg501Lys
  • NC_000012.11:g.112926882G>A
  • NM_002834.3:c.1502G>A
  • NM_002834.4:c.1502G>A
  • NM_080601.1:c.*2445G>A
  • c.1502G>A
Protein change:
R500K
Links:
dbSNP: rs397507543
NCBI 1000 Genomes Browser:
rs397507543
Molecular consequence:
  • NM_001330437.2:c.1514G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374625.1:c.1499G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_002834.5:c.1502G>A - missense variant - [Sequence Ontology: SO:0001583]
Observations:
6

Condition(s)

Name:
Noonan syndrome (NS)
Synonyms:
Noonan's syndrome; Pseudo-Turner syndrome
Identifiers:
MONDO: MONDO:0018997; MeSH: D009634; MedGen: C0028326; OMIM: PS163950

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000061280Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
criteria provided, single submitter

(LMM Criteria)
Pathogenic
(Jan 26, 2016)
germlineclinical testing

PubMed (6)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot provided76not providednot providednot providedclinical testing

Citations

PubMed

The mutational spectrum of PTPN11 in juvenile myelomonocytic leukemia and Noonan syndrome/myeloproliferative disease.

Kratz CP, Niemeyer CM, Castleberry RP, Cetin M, Bergsträsser E, Emanuel PD, Hasle H, Kardos G, Klein C, Kojima S, Stary J, Trebo M, Zecca M, Gelb BD, Tartaglia M, Loh ML.

Blood. 2005 Sep 15;106(6):2183-5. Epub 2005 May 31.

PubMed [citation]
PMID:
15928039
PMCID:
PMC1895140

PTPN11 mutations in Noonan syndrome: molecular spectrum, genotype-phenotype correlation, and phenotypic heterogeneity.

Tartaglia M, Kalidas K, Shaw A, Song X, Musat DL, van der Burgt I, Brunner HG, Bertola DR, Crosby A, Ion A, Kucherlapati RS, Jeffery S, Patton MA, Gelb BD.

Am J Hum Genet. 2002 Jun;70(6):1555-63. Epub 2002 May 1.

PubMed [citation]
PMID:
11992261
PMCID:
PMC379142
See all PubMed Citations (6)

Details of each submission

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000061280.6

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided7not providednot providedclinical testing PubMed (6)

Description

The p.Arg501Lys variant in PTPN11 has been reported in >10 individuals with the clinical features of Noonan syndrome and segregated with disease in 1 affected r elative (Tartaglia 2002, Limal 2006, Noordam 2008, Jefferies 2010, LMM unpublish ed data). It has not been identified in large population studies. In summary, th is variant meets our criteria to be classified as pathogenic for Noonan syndrome in an autosomal dominant manner based upon presence in multiple affected indivi duals, segregation studies, and absence in the general population.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot provided7not provided6not provided

Last Updated: May 19, 2024