NM_002834.5(PTPN11):c.1505C>T (p.Ser502Leu) AND not provided

Germline classification:: Pathogenic (4 submissions)
Last evaluated:: Aug 1, 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:: RCV000033544.28

Allele description [Variation Report for NM_002834.5(PTPN11):c.1505C>T (p.Ser502Leu)]

NM_002834.5(PTPN11):c.1505C>T (p.Ser502Leu)

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.1505C>T (p.Ser502Leu)

Other names:

p.S502L:TCA>TTA

HGVS:

NC_000012.12:g.112489081C>T
NG_007459.1:g.75350C>T
NM_001330437.2:c.1517C>T
NM_001374625.1:c.1502C>T
NM_002834.5:c.1505C>TMANE SELECT
NP_001317366.1:p.Ser506Leu
NP_001361554.1:p.Ser501Leu
NP_002825.3:p.Ser502Leu
NP_002825.3:p.Ser502Leu
LRG_614t1:c.1505C>T
LRG_614:g.75350C>T
LRG_614p1:p.Ser502Leu
NC_000012.11:g.112926885C>T
NM_002834.3:c.1505C>T
NM_002834.4:c.1505C>T
NM_080601.1:c.*2448C>T
c.1505C>T

Protein change:

S501L

Links:

dbSNP: rs397507544

NCBI 1000 Genomes Browser:

rs397507544

Molecular consequence:

NM_001330437.2:c.1517C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001374625.1:c.1502C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_002834.5:c.1505C>T - missense variant - [Sequence Ontology: SO:0001583]

Observations:

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
SCV000057449	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (May 18, 2022)	germline	clinical testing	Citation Link,
SCV001740219	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus	no assertion criteria provided	Pathogenic	germline	clinical testing
SCV001953570	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Pathogenic	germline	clinical testing
SCV004033226	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Pathogenic (Aug 1, 2023)	germline	clinical testing	Citation Link

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Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	1	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000057449.18

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

Description

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: 28628100, 28084675, 24030381, 18948947, 17910045, 15385933, 28183348, 26918529, 18470943, 17020470, 16358218, 19020799, 24803665, 28991257, 30050098, 30287924, 29907801, 32164556, 31115076, 33318624, 29493581, 32368696)

#	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 Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus, SCV001740219.3

#	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	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ - VKGL Data-share Consensus, SCV001953570.1

#	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	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From CeGaT Center for Human Genetics Tuebingen, SCV004033226.11

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

Description

PTPN11: PS2:Very Strong, PM2, PM5, PP3

#	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		1	not provided	not provided	not provided

Last Updated: Nov 24, 2024

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