NM_015466.4(PTPN23):c.1291C>T (p.Arg431Trp) AND not provided

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 1, 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:: RCV001869201.2

Allele description

NM_015466.4(PTPN23):c.1291C>T (p.Arg431Trp)

Gene:

PTPN23:protein tyrosine phosphatase non-receptor type 23 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3p21.31

Genomic location:

Preferred name:

NM_015466.4(PTPN23):c.1291C>T (p.Arg431Trp)

HGVS:

NC_000003.12:g.47408451C>T
NG_051056.1:g.32470C>T
NM_001304482.2:c.913C>T
NM_015466.4:c.1291C>TMANE SELECT
NP_001291411.1:p.Arg305Trp
NP_056281.1:p.Arg431Trp
NC_000003.11:g.47449941C>T

Protein change:

R305W

Links:

dbSNP: rs150712932

NCBI 1000 Genomes Browser:

rs150712932

Molecular consequence:

NM_001304482.2:c.913C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_015466.4:c.1291C>T - 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
SCV002180084	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Sep 1, 2022)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 31395947, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002180084

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Sep 1, 2022)

germline

clinical testing

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

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

Phenotype and mutation expansion of the PTPN23 associated disorder characterized by neurodevelopmental delay and structural brain abnormalities.

Bend R, Cohen L, Carter MT, Lyons MJ, Niyazov D, Mikati MA, Rojas SK, Person RE, Si Y, Wentzensen IM; Regeneron Genetics Center., Torti E, Lee JA, Boycott KM, Basel-Salmon L, Ferreira CR, Gonzaga-Jauregui C.

Eur J Hum Genet. 2020 Jan;28(1):76-87. doi: 10.1038/s41431-019-0487-1. Epub 2019 Aug 8.

PubMed [citation]

PMID:: 31395947
PMCID:: PMC6906308

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 Invitae, SCV002180084.2

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

Description

This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 431 of the PTPN23 protein (p.Arg431Trp). This variant is present in population databases (rs150712932, gnomAD 0.03%). This missense change has been observed in individual(s) with clinical features of PTPN23-related conditions (PMID: 31395947). ClinVar contains an entry for this variant (Variation ID: 636317). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Not Available"; Align-GVGD: "Class C0"). 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.

#	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: Mar 16, 2024

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