NM_002834.5(PTPN11):c.214G>A (p.Ala72Thr) AND not provided

Germline classification:: Pathogenic (3 submissions)
Last evaluated:: Sep 18, 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:: RCV000680626.8

Allele description [Variation Report for NM_002834.5(PTPN11):c.214G>A (p.Ala72Thr)]

NM_002834.5(PTPN11):c.214G>A (p.Ala72Thr)

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.214G>A (p.Ala72Thr)

HGVS:

NC_000012.12:g.112450394G>A
NG_007459.1:g.36663G>A
NM_001330437.2:c.214G>A
NM_001374625.1:c.211G>A
NM_002834.5:c.214G>AMANE SELECT
NM_080601.3:c.214G>A
NP_001317366.1:p.Ala72Thr
NP_001361554.1:p.Ala71Thr
NP_002825.3:p.Ala72Thr
NP_542168.1:p.Ala72Thr
LRG_614t1:c.214G>A
LRG_614:g.36663G>A
NC_000012.11:g.112888198G>A
NM_002834.3:c.214G>A
Q06124:p.Ala72Thr

Protein change:

A71T

Links:

UniProtKB: Q06124#VAR_015996; dbSNP: rs121918453

NCBI 1000 Genomes Browser:

rs121918453

Molecular consequence:

NM_001330437.2:c.214G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374625.1:c.211G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_002834.5:c.214G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_080601.3:c.214G>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
SCV000808069	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Sep 18, 2023)	germline	clinical testing	Citation Link,
SCV001952190	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	Likely pathogenic	germline	clinical testing
SCV001964020	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Pathogenic	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000808069

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Sep 18, 2023)

germline

clinical testing

Citation Link,

SCV001952190

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

See additional submitters

no assertion criteria provided

Likely pathogenic

germline

clinical testing

SCV001964020

Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus

See additional submitters

no assertion criteria provided

Pathogenic

germline

clinical testing

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

Details of each submission

From GeneDx, SCV000808069.2

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

Description

Frequently observed as a somatic variant in patients with juvenile myelomonocytic leukemia (JMML), acute myeloid leukemia (AML), and/or myelodysplastic syndrome (MDS) (Tartaglia et al., 2003; Kratz et al., 2005; Tartaglia et al., 2006; Christiansen et al., 2007; Hou et al., 2008; Park et al., 2012; Stasik et al., 2021); Not observed at significant frequency in large population cohorts (gnomAD); Missense variants in this gene are often considered pathogenic (HGMD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 17972951, 12634870, 16518851, 21901340, 12717436, 14982869, 16358218, 17330262, 17353900, 28098151, 11992261, 9491886, 16053901, 29493581, 32786180, 34411415, 34958143, 34459887, 30868567, 15928039)

#	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, SCV001952190.1

#	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 Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus, SCV001964020.1

#	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

Last Updated: Sep 16, 2024

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