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NM_002834.5(PTPN11):c.174C>A (p.Asn58Lys) AND not provided

Germline classification:
Pathogenic (2 submissions)
Last evaluated:
Jun 24, 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:
RCV000157677.6

Allele description [Variation Report for NM_002834.5(PTPN11):c.174C>A (p.Asn58Lys)]

NM_002834.5(PTPN11):c.174C>A (p.Asn58Lys)

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.174C>A (p.Asn58Lys)
Other names:
p.N58K:AAC>AAA
HGVS:
  • NC_000012.12:g.112450354C>A
  • NG_007459.1:g.36623C>A
  • NM_001330437.2:c.174C>A
  • NM_001374625.1:c.171C>A
  • NM_002834.5:c.174C>AMANE SELECT
  • NM_080601.3:c.174C>A
  • NP_001317366.1:p.Asn58Lys
  • NP_001361554.1:p.Asn57Lys
  • NP_002825.3:p.Asn58Lys
  • NP_542168.1:p.Asn58Lys
  • LRG_614t1:c.174C>A
  • LRG_614:g.36623C>A
  • NC_000012.11:g.112888158C>A
  • NM_002834.3:c.174C>A
  • Q06124:p.Asn58Lys
  • c.174C>A
Protein change:
N57K
Links:
UniProtKB: Q06124#VAR_027184; dbSNP: rs397507506
NCBI 1000 Genomes Browser:
rs397507506
Molecular consequence:
  • NM_001330437.2:c.174C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374625.1:c.171C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_002834.5:c.174C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_080601.3:c.174C>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000057361GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)
Pathogenic
(Jun 24, 2023)
germlineclinical testing

Citation Link,

SCV000207648Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center
no assertion criteria provided
Pathogenic
(Jan 15, 2015)
germlineclinical testing

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000057361.14

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

Description

In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Missense variants in this gene are often considered pathogenic (HGMD); Multiple pathogenic missense variants at this residue (p.N58D, p.N58Y, p.N58H) have been reported in association with Noonan spectrum disorders; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 34184824, 26633542, 29212898, 28911804, 30050098, 29907801, 11992261, 9491886, 16053901, 29493581, 34782754)

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

From Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center, SCV000207648.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024