NM_015466.4(PTPN23):c.3484C>T (p.Arg1162Trp) AND Neurodevelopmental disorder and structural brain anomalies with or without seizures and spasticity

Germline classification:: Likely benign (1 submission)
Last evaluated:: Nov 17, 2023
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:: RCV003492739.2

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:: Neurodevelopmental disorder and structural brain anomalies with or without seizures and spasticity
Identifiers:: MONDO: MONDO:0030046; MedGen: C5394423; OMIM: 618890

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004237868	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Nov 17, 2023)	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

SCV004237868

Revvity Omics, Revvity

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely benign
(Nov 17, 2023)

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

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Revvity Omics, Revvity, SCV004237868.1

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

#	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: May 19, 2024

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