NM_002834.5(PTPN11):c.417G>T (p.Glu139Asp) AND Inborn genetic diseases

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 21, 2017
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:: RCV001267275.2

Allele description [Variation Report for NM_002834.5(PTPN11):c.417G>T (p.Glu139Asp)]

NM_002834.5(PTPN11):c.417G>T (p.Glu139Asp)

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.417G>T (p.Glu139Asp)

Other names:

p.E139D:GAG>GAT

HGVS:

NC_000012.12:g.112453279G>T
NG_007459.1:g.39548G>T
NM_001330437.2:c.417G>T
NM_001374625.1:c.414G>T
NM_002834.5:c.417G>TMANE SELECT
NM_080601.3:c.417G>T
NP_001317366.1:p.Glu139Asp
NP_001361554.1:p.Glu138Asp
NP_002825.3:p.Glu139Asp
NP_542168.1:p.Glu139Asp
LRG_614t1:c.417G>T
LRG_614:g.39548G>T
NC_000012.11:g.112891083G>T
NM_002834.3:c.417G>T
NM_080601.1:c.417G>T
Q06124:p.Glu139Asp
c.417G>T

Protein change:

E138D

Links:

UniProtKB: Q06124#VAR_015613; dbSNP: rs397507520

NCBI 1000 Genomes Browser:

rs397507520

Molecular consequence:

NM_001330437.2:c.417G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001374625.1:c.414G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_002834.5:c.417G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_080601.3:c.417G>T - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Name:: Inborn genetic diseases
Identifiers:: MeSH: D030342; MedGen: C0950123

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001445456	Ambry Genetics	criteria provided, single submitter (Ambry exome assertion method (8-5-2015))	Pathogenic (Dec 21, 2017)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 11992261, 18372317 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001445456

Ambry Genetics

criteria provided, single submitter

(Ambry exome assertion method (8-5-2015))

Pathogenic
(Dec 21, 2017)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

Citation Link

Help

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	1	not provided	clinical testing
Asian/Caucasian	germline	yes	1	not provided	not provided	1	not provided	clinical testing

Citations

PubMed

PTPN11 mutations in Noonan syndrome: molecular spectrum, genotype-phenotype correlation, and phenotypic heterogeneity.

Tartaglia M, Kalidas K, Shaw A, Song X, Musat DL, van der Burgt I, Brunner HG, Bertola DR, Crosby A, Ion A, Kucherlapati RS, Jeffery S, Patton MA, Gelb BD.

Am J Hum Genet. 2002 Jun;70(6):1555-63. Epub 2002 May 1.

PubMed [citation]

PMID:: 11992261
PMCID:: PMC379142

Diverse driving forces underlie the invariant occurrence of the T42A, E139D, I282V and T468M SHP2 amino acid substitutions causing Noonan and LEOPARD syndromes.

Martinelli S, Torreri P, Tinti M, Stella L, Bocchinfuso G, Flex E, Grottesi A, Ceccarini M, Palleschi A, Cesareni G, Castagnoli L, Petrucci TC, Gelb BD, Tartaglia M.

Hum Mol Genet. 2008 Jul 1;17(13):2018-29. doi: 10.1093/hmg/ddn099. Epub 2008 Mar 27.

PubMed [citation]

PMID:: 18372317
PMCID:: PMC2900904

Details of each submission

From Ambry Genetics, SCV001445456.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	PubMed (2)
2	Asian/Caucasian	1	not provided	not provided	clinical testing	PubMed (2)

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

Last Updated: Sep 29, 2024

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