NM_002834.5(PTPN11):c.1504T>A (p.Ser502Thr) AND not provided

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Jan 10, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000212897.12

Allele description [Variation Report for NM_002834.5(PTPN11):c.1504T>A (p.Ser502Thr)]

NM_002834.5(PTPN11):c.1504T>A (p.Ser502Thr)

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.1504T>A (p.Ser502Thr)

Other names:

p.S502T:TCA>ACA

HGVS:

NC_000012.12:g.112489080T>A
NG_007459.1:g.75349T>A
NM_001330437.2:c.1516T>A
NM_001374625.1:c.1501T>A
NM_002834.5:c.1504T>AMANE SELECT
NP_001317366.1:p.Ser506Thr
NP_001361554.1:p.Ser501Thr
NP_002825.3:p.Ser502Thr
LRG_614t1:c.1504T>A
LRG_614:g.75349T>A
NC_000012.11:g.112926884T>A
NM_001330437.2:c.1516T>A
NM_002834.3:c.1504T>A
NM_002834.4:c.1504T>A

Protein change:

S501T; SER502THR

Links:

OMIM: 176876.0007; dbSNP: rs121918458

NCBI 1000 Genomes Browser:

rs121918458

Molecular consequence:

NM_001330437.2:c.1516T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374625.1:c.1501T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_002834.5:c.1504T>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000057448	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Jan 10, 2023)	germline	clinical testing	Citation Link,
SCV000927150	Blueprint Genetics	criteria provided, single submitter (Blueprint Genetics Variant Classification Scheme)	Pathogenic (Feb 14, 2017)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000057448

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Jan 10, 2023)

germline

clinical testing

Citation Link,

SCV000927150

Blueprint Genetics

criteria provided, single submitter

(Blueprint Genetics Variant Classification Scheme)

Pathogenic
(Feb 14, 2017)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000057448.14

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

Published functional studies demonstrate a significant increase in phosphatase activity compared wildtype (Niihori et al., 2005); Not observed in large population cohorts (gnomAD); 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); This variant is associated with the following publications: (PMID: 16358218, 15240615, 27521173, 12739139, 34184824, 12325025, 24803665, 15834506, 21407260, 25862627, 19737548, 32164556)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Blueprint Genetics, SCV000927150.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Apr 6, 2024

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