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

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Dec 13, 2021
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:
RCV001800333.9

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:
1

Condition(s)

Name:
Epicanthus
Synonyms:
Epicanthal fold
Identifiers:
MedGen: C0678230; OMIM: 131500; Human Phenotype Ontology: HP:0000286
Name:
Short stature
Identifiers:
MedGen: C0349588; Human Phenotype Ontology: HP:0004322
Name:
Abnormal cardiovascular system morphology
Synonyms:
Abnormality of cardiovascular system morphology
Identifiers:
MedGen: C4049796; Human Phenotype Ontology: HP:0030680
Name:
Abnormal pinna morphology
Synonyms:
Abnormality of the pinna; Bilateral external ear deformity
Identifiers:
MedGen: C0857379; Human Phenotype Ontology: HP:0000377
Name:
Wide nasal bridge
Identifiers:
MedGen: C1849367; Human Phenotype Ontology: HP:0000431
Name:
Microcephaly
Synonyms:
Microcephaly (disease)
Identifiers:
MONDO: MONDO:0001149; MedGen: C4551563; Human Phenotype Ontology: HP:0000252
Name:
Depressed nasal ridge
Identifiers:
MedGen: C1842876; Human Phenotype Ontology: HP:0000457

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV002047380Institute of Human Genetics, University Hospital Muenster
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Dec 13, 2021)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not 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 Institute of Human Genetics, University Hospital Muenster, SCV002047380.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)

Description

ACMG categories: PM1,PM2,PP3,PP4,PP5

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providedbloodnot provided1not providednot providednot provided

Last Updated: Jun 23, 2024