NM_002834.5(PTPN11):c.209A>G (p.Lys70Arg) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Sep 20, 2024
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:: RCV000405696.4

Allele description [Variation Report for NM_002834.5(PTPN11):c.209A>G (p.Lys70Arg)]

NM_002834.5(PTPN11):c.209A>G (p.Lys70Arg)

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.209A>G (p.Lys70Arg)

HGVS:

NC_000012.12:g.112450389A>G
NG_007459.1:g.36658A>G
NM_001330437.2:c.209A>G
NM_001374625.1:c.206A>G
NM_002834.5:c.209A>GMANE SELECT
NM_080601.3:c.209A>G
NP_001317366.1:p.Lys70Arg
NP_001361554.1:p.Lys69Arg
NP_002825.3:p.Lys70Arg
NP_542168.1:p.Lys70Arg
LRG_614t1:c.209A>G
LRG_614:g.36658A>G
NC_000012.11:g.112888193A>G
NM_002834.3:c.209A>G
NM_002834.4:c.209A>G
NM_002834.5(PTPN11):c.209A>GMANE SELECT
c.209A>G

Protein change:

K69R

Links:

dbSNP: rs397516801

NCBI 1000 Genomes Browser:

rs397516801

Molecular consequence:

NM_001330437.2:c.209A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001374625.1:c.206A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_002834.5:c.209A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_080601.3:c.209A>G - 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
SCV000329577	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Sep 20, 2024)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000329577

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Sep 20, 2024)

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

Details of each submission

From GeneDx, SCV000329577.8

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

Description

Observed in multiple individuals with a PTPN11-related disorder in the published literature, and in patients previously tested at GeneDx (PMID: 30050098, 29084544); Not observed in large population cohorts (gnomAD); Missense variants in this gene are a common cause of disease and they are underrepresented in the general population; In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 34346503, 29084544, 30050098, 29907801, 32037394, 34358384, 11992261, 9491886, 16053901, 29493581)

#	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: Oct 8, 2024

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