NM_002834.5(PTPN11):c.1039C>A (p.Gln347Lys) AND RASopathy

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Apr 29, 2022
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:: RCV001933107.6

Allele description [Variation Report for NM_002834.5(PTPN11):c.1039C>A (p.Gln347Lys)]

NM_002834.5(PTPN11):c.1039C>A (p.Gln347Lys)

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.1039C>A (p.Gln347Lys)

HGVS:

NC_000012.12:g.112477962C>A
NG_007459.1:g.64231C>A
NM_001330437.2:c.1039C>A
NM_001374625.1:c.1036C>A
NM_002834.5:c.1039C>AMANE SELECT
NM_080601.3:c.1039C>A
NP_001317366.1:p.Gln347Lys
NP_001361554.1:p.Gln346Lys
NP_002825.3:p.Gln347Lys
NP_542168.1:p.Gln347Lys
LRG_614:g.64231C>A
NC_000012.11:g.112915766C>A

Protein change:

Q346K

Links:

dbSNP: rs2038533750

NCBI 1000 Genomes Browser:

rs2038533750

Molecular consequence:

NM_001330437.2:c.1039C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374625.1:c.1036C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_002834.5:c.1039C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_080601.3:c.1039C>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: RASopathy
Synonyms:: rasopathies; Noonan spectrum disorder
Identifiers:: MONDO: MONDO:0021060; MedGen: C5555857

Recent activity

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Cela2a chymotrypsin like elastase 2A [Rattus norvegicus]
Cela2a chymotrypsin like elastase 2A [Rattus norvegicus]
Gene ID:24332

Gene
24332[uid] AND (alive[prop]) (1)
Gene
D17Jcs85 DNA segment, Chr 17, John C. Schimenti 85 [Mus musculus]
D17Jcs85 DNA segment, Chr 17, John C. Schimenti 85 [Mus musculus]
Gene ID:360070

Gene
Listeria monocytogenes strain Lm14 contig000021, whole genome shotgun sequence
Listeria monocytogenes strain Lm14 contig000021, whole genome shotgun sequence
gi|1058471706|gb|MDMA01000021.1||gn :MDMA01|contig000021

Nucleotide
Francisella noatunensis strain FSC1142 FSC1142_71_len5141, whole genome shotgun ...
Francisella noatunensis strain FSC1142 FSC1142_71_len5141, whole genome shotgun sequence
gi|1956172827|ref|NZ_JACVKP01000007 gnl|WGS:NZ_JACVKP01|FSC1142_71_len5141

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002188713	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Apr 29, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002188713

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Apr 29, 2022)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002188713.3

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

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt PTPN11 protein function. This variant has not been reported in the literature in individuals affected with PTPN11-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces glutamine, which is neutral and polar, with lysine, which is basic and polar, at codon 347 of the PTPN11 protein (p.Gln347Lys).

#	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: Sep 29, 2024

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