PTPN23 protein tyrosine phosphatase non-receptor type 23 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PTPN23provided by HGNC
Official Full Name: protein tyrosine phosphatase non-receptor type 23provided by HGNC
Primary source: HGNC:HGNC:14406
See related: Ensembl:ENSG00000076201 MIM:606584; AllianceGenome:HGNC:14406
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: HDPTP; HD-PTP; NEDBASS; PTP-TD14
Summary: This gene encodes a member of the non-receptor type protein-tyrosine phosphatase family. The encoded protein may be involved in the regulation of small nuclear ribonucleo protein assembly and pre-mRNA splicing by modifying the survival motor neuron (SMN) complex. The encoded protein additionally plays a role in ciliogenesis and is part of endosomal sorting complex required for transport (ESCRT) pathways. This gene may serve a tumor suppressor function. [provided by RefSeq, Jul 2016]
Expression: Ubiquitous expression in spleen (RPKM 10.2), brain (RPKM 9.8) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 3p21.31

Exon count:: 25

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (47381021..47413435)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (47397442..47429855)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (47422511..47454925)

Chromosome 3 - NC_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

PTPN23[Thr] variant reduces susceptibility and tumorigenesis in esophageal squamous cell carcinoma through dephosphorylation of EGFR.
Title: PTPN23[Thr] variant reduces susceptibility and tumorigenesis in esophageal squamous cell carcinoma through dephosphorylation of EGFR.
PTPN23 ubiquitination by WDR4 suppresses EGFR and c-MET degradation to define a lung cancer therapeutic target.
Title: PTPN23 ubiquitination by WDR4 suppresses EGFR and c-MET degradation to define a lung cancer therapeutic target.
Interactions of ubiquitin and CHMP5 with the V domain of HD-PTP reveals role for regulation of Vps4 ATPase.
Title: Interactions of ubiquitin and CHMP5 with the V domain of HD-PTP reveals role for regulation of Vps4 ATPase.
Phenotype and mutation expansion of the PTPN23 associated disorder characterized by neurodevelopmental delay and structural brain abnormalities.
Title: Phenotype and mutation expansion of the PTPN23 associated disorder characterized by neurodevelopmental delay and structural brain abnormalities.
Our report provides the first description of the clinical phenotype of recessive PTPN23 variants with pathogenicity substantiated by a functional study
Title: Developmental epileptic encephalopathy with hypomyelination and brain atrophy associated with PTPN23 variants affecting the assembly of UsnRNPs.
Mutations in PTPN23 gene is associated with developmental and epileptic encephalopathy.
Title: Mutations of PTPN23 in developmental and epileptic encephalopathy.
HD-PTP/PTPN23 as a prominent haploinsufficient tumor suppressor gene preventing tumor progression through control of integrin trafficking.
Title: Haploinsufficiency of the ESCRT Component HD-PTP Predisposes to Cancer.
the underlying mechanism of PTPN23 function in breast tumorigenesis as that of a key phosphatase that normally suppresses the activity of FYN
Title: Suppression of protein tyrosine phosphatase N23 predisposes to breast tumorigenesis via activation of FYN kinase.
The role of HD-PTP/PTPN23 in cancer and tumorigenesis is reviewed.
Title: Role of ESCRT component HD-PTP/PTPN23 in cancer.
Results present crystal structures of the coiled-coil domain of the HD-PTP phosphatase and its complex with UBAP1. The coiled-coil domain adopts an unexpected open and rigid conformation. The HD-PTP:UBAP1 structure identifies the molecular determinants of the interaction and provides a molecular basis for the specific functional cooperation between HD-PTP and UBAP1.
Title: Structural Basis for Selective Interaction between the ESCRT Regulator HD-PTP and UBAP1.

Submit: New GeneRIF Correction See all GeneRIFs (24)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Neurodevelopmental disorder and structural brain anomalies with or without seizures and spasticity MedGen: C5394423 OMIM: 618890 GeneReviews: Not available	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Pr55(Gag)	gag	The isolated Bro1 domains of HD-PTP and rhophilin both bind to HIV-1 NC and share the capacity to stimulate VLP production by a minimal HIV-1 Gag molecule	PubMed
Tat	tat	HIV-1 Tat upregulates the tyrosine phosphatase HD-PTP mRNA in a human endothelial cell line, however Tat-induction of HD-PTP mRNA parallels only with a slight increase of the protein	PubMed
nucleocapsid	gag	The isolated Bro1 domains of HD-PTP and rhophilin both bind to HIV-1 NC and share the capacity to stimulate VLP production by a minimal HIV-1 Gag molecule	PubMed

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

G16531 (e-PCR)
- UniSTS:19969

RH47493 (e-PCR)
- UniSTS:76657

PTPN23_1258 (e-PCR)
- UniSTS:277624

RH91891 (e-PCR)
- UniSTS:88778

SHGC-76917 (e-PCR)
- UniSTS:49149

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables histone H2AXY142 phosphatase activity	IEA Inferred from Electronic Annotation more info
enables non-membrane spanning protein tyrosine phosphatase activity	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein kinase binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein tyrosine phosphatase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables protein tyrosine phosphatase activity, metal-dependent	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in cilium assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in early endosome to late endosome transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in early endosome to late endosome transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in endocytic recycling	IBA Inferred from Biological aspect of Ancestor more info
involved_in endocytic recycling	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of epithelial cell migration	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of Wnt protein secretion	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of adherens junction organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of early endosome to late endosome transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of homophilic cell adhesion	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in ciliary basal body	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in early endosome	IDA Inferred from Direct Assay more info	PubMed
is_active_in endosome	IBA Inferred from Biological aspect of Ancestor more info
located_in endosome	IDA Inferred from Direct Assay more info	PubMed
located_in extracellular exosome	HDA more info	PubMed
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info
located_in nuclear body	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: tyrosine-protein phosphatase non-receptor type 23

Names: his domain-containing protein tyrosine phosphatase; protein tyrosine phosphatase TD14

NP_001291411.1

EC 3.1.3.48

NP_056281.1

EC 3.1.3.48

XP_005265088.2

EC 3.1.3.48

XP_054202077.1

EC 3.1.3.48

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_051056.1 RefSeqGene

Range

5040..37454

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001304482.2 → NP_001291411.1 tyrosine-protein phosphatase non-receptor type 23 isoform 2

See identical proteins and their annotated locations for NP_001291411.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an alternate exon in its 5' UTR and uses a downstream start codon compared to variant 1. It encodes isoform 2 which has a shorter N-terminus compared to isoform 1.

Source sequence(s)

AF290614, AK299906, BU173747

UniProtKB/TrEMBL

B4DST5

Conserved Domains (5) summary

cd09234
Location:236 → 574

V_HD-PTP_like; Protein-interacting V-domain of mammalian His-Domain type N23 protein tyrosine phosphatase and related domains

cd00047
Location:1094 → 1323

PTPc; Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr ...

pfam00102
Location:1094 → 1324

Y_phosphatase; Protein-tyrosine phosphatase

pfam13949
Location:291 → 575

ALIX_LYPXL_bnd; ALIX V-shaped domain binding to HIV

cl14649
Location:1 → 231

BRO1_Alix_like; Protein-interacting Bro1-like domain of mammalian Alix and related domains
NM_015466.4 → NP_056281.1 tyrosine-protein phosphatase non-receptor type 23 isoform 1

See identical proteins and their annotated locations for NP_056281.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AB040904, AF290614, BU173747

Consensus CDS

CCDS2754.1

UniProtKB/Swiss-Prot

A8K0D7, Q7KZF8, Q8N6Z5, Q9BSR5, Q9H3S7, Q9P257, Q9UG03, Q9UMZ4

Related

ENSP00000265562.4, ENST00000265562.5

Conserved Domains (5) summary

cd09234
Location:362 → 700

V_HD-PTP_like; Protein-interacting V-domain of mammalian His-Domain type N23 protein tyrosine phosphatase and related domains

cd09239
Location:2 → 357

BRO1_HD-PTP_like; Protein-interacting, N-terminal, Bro1-like domain of mammalian His-Domain type N23 protein tyrosine phosphatase and related domains

cd00047
Location:1220 → 1449

PTPc; Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr ...

pfam00102
Location:1220 → 1450

Y_phosphatase; Protein-tyrosine phosphatase

pfam13949
Location:417 → 701

ALIX_LYPXL_bnd; ALIX V-shaped domain binding to HIV

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000003.12 Reference GRCh38.p14 Primary Assembly

Range

47381021..47413435

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005265031.3 → XP_005265088.2 tyrosine-protein phosphatase non-receptor type 23 isoform X1

Conserved Domains (5) summary

cd09234
Location:352 → 690

V_HD-PTP_like; Protein-interacting V-domain of mammalian His-Domain type N23 protein tyrosine phosphatase and related domains

cd09239
Location:2 → 347

BRO1_HD-PTP_like; Protein-interacting, N-terminal, Bro1-like domain of mammalian His-Domain type N23 protein tyrosine phosphatase and related domains

cd00047
Location:1210 → 1439

PTPc; Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr ...

pfam00102
Location:1210 → 1440

Y_phosphatase; Protein-tyrosine phosphatase

pfam13949
Location:407 → 691

ALIX_LYPXL_bnd; ALIX V-shaped domain binding to HIV