NM_015466.4(PTPN23):c.3484C>T (p.Arg1162Trp) AND PTPN23-related disorder

Germline classification:: Likely benign (1 submission)
Last evaluated:: Sep 7, 2022
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

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:: RCV003958877.2

Allele description [Variation Report for NM_015466.4(PTPN23):c.3484C>T (p.Arg1162Trp)]

NM_015466.4(PTPN23):c.3484C>T (p.Arg1162Trp)

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.3484C>T (p.Arg1162Trp)

HGVS:

NC_000003.12:g.47411282C>T
NG_051056.1:g.35301C>T
NM_001304482.2:c.3106C>T
NM_015466.4:c.3484C>TMANE SELECT
NP_001291411.1:p.Arg1036Trp
NP_056281.1:p.Arg1162Trp
NC_000003.11:g.47452772C>T
NM_015466.3:c.3484C>T

Protein change:

R1036W

Links:

dbSNP: rs147400377

NCBI 1000 Genomes Browser:

rs147400377

Molecular consequence:

NM_001304482.2:c.3106C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_015466.4:c.3484C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: PTPN23-related disorder
Synonyms:: PTPN23-related condition
Identifiers:

Recent activity

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Chain A, Pyrroline-5-carboxylate reductase
Chain A, Pyrroline-5-carboxylate reductase
gi|347948775|pdb|3TRI|A

Protein
SYN3 [Gorilla gorilla gorilla]
SYN3 [Gorilla gorilla gorilla]
Gene ID:101145710

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004774085	PreventionGenetics, part of Exact Sciences	no assertion criteria provided	Likely benign (Sep 7, 2022)	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004774085

PreventionGenetics, part of Exact Sciences

no assertion criteria provided

Likely benign
(Sep 7, 2022)

germline

clinical testing

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

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV004774085.2

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

Description

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).

#	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: Oct 13, 2024

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