Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	25930
Gene name Gene Name - the full gene name approved by the HGNC.	Protein tyrosine phosphatase non-receptor type 23
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	PTPN23
Synonyms (NCBI Gene) Gene synonyms aliases	HD-PTP, HDPTP, NEDBASS, PTP-TD14
Chromosome Chromosome number	3
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	3p21.31
Summary Summary of gene provided in NCBI Entrez Gene.	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)

Show/Hide all(12)

SNP ID	Visualize variation	Clinical significance	Consequence
rs138076291	C>G,T	Likely-pathogenic	Missense variant, coding sequence variant
rs147293860	A>C,G	Likely-pathogenic	Coding sequence variant, missense variant
rs148689441	G>A	Likely-pathogenic	Coding sequence variant, missense variant
rs150712932	C>T	Likely-pathogenic	Coding sequence variant, missense variant
rs577689618	G>A,T	Likely-pathogenic	Missense variant, coding sequence variant
rs730882229	G>A,T	Likely-pathogenic	Missense variant, coding sequence variant
rs751809435	AAG>-	Likely-pathogenic	Coding sequence variant, inframe deletion
rs760022693	CAGCCCCATCCT>-,CAGCCCCATCCTCAGCCCCATCCT	Likely-pathogenic	Inframe deletion, inframe insertion, coding sequence variant
rs770692989	A>G	Likely-pathogenic	Coding sequence variant, missense variant
rs779096974	AGTTGCAGGTCTCCCCTCGGCCCCACC>-,AGTTGCAGGTCTCCCCTCGGCCCCACCAGTTGCAGGTCTCCCCTCGGCCCCACC	Likely-pathogenic	Inframe insertion, inframe deletion, coding sequence variant
rs967738491	C>T	Likely-pathogenic	Missense variant, coding sequence variant
rs1576235873	->CC	Likely-pathogenic	Frameshift variant, coding sequence variant

Show/Hide all(7)

miRTarBase ID	miRNA	Experiments	Reference
MIRT051946	hsa-let-7b-5p	CLASH	23622248
MIRT050524	hsa-miR-20a-5p	CLASH	23622248
MIRT048027	hsa-miR-148a-3p	CLASH	23622248
MIRT053242	hsa-miR-142-3p	Luciferase reporter assay, qRT-PCR, Western blot	23843459
MIRT2081113	hsa-miR-1912	CLIP-seq
MIRT2081113	hsa-miR-1912	CLIP-seq
MIRT2457454	hsa-miR-596	CLIP-seq

Show/Hide all(40)

GO ID	Ontology	Definition	Evidence	Reference
GO:0004721	Function	Phosphoprotein phosphatase activity	IEA
GO:0004725	Function	Protein tyrosine phosphatase activity	IEA
GO:0004725	Function	Protein tyrosine phosphatase activity	IMP	21724833
GO:0005515	Function	Protein binding	IPI	17174262, 18434552, 18835089, 19523899, 20936779, 21179510, 21724833, 25416956, 28514442, 31515488, 32079660, 32296183, 33961781
GO:0005634	Component	Nucleus	IDA	21179510
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005737	Component	Cytoplasm	IDA	21179510
GO:0005737	Component	Cytoplasm	IEA
GO:0005768	Component	Endosome	IBA
GO:0005768	Component	Endosome	IDA	21179510
GO:0005768	Component	Endosome	IEA
GO:0005769	Component	Early endosome	IDA	21757351
GO:0005769	Component	Early endosome	IEA
GO:0005829	Component	Cytosol	IDA
GO:0005856	Component	Cytoskeleton	IEA
GO:0005929	Component	Cilium	IEA
GO:0010633	Process	Negative regulation of epithelial cell migration	IMP	21724833
GO:0015031	Process	Protein transport	IEA
GO:0016604	Component	Nuclear body	IDA
GO:0016787	Function	Hydrolase activity	IEA
GO:0019901	Function	Protein kinase binding	IPI	21724833
GO:0030030	Process	Cell projection organization	IEA
GO:0031410	Component	Cytoplasmic vesicle	IEA
GO:0032456	Process	Endocytic recycling	IBA
GO:0032456	Process	Endocytic recycling	IMP	24821423
GO:0034451	Component	Centriolar satellite	IDA
GO:0036064	Component	Ciliary basal body	IDA	20393563
GO:0042995	Component	Cell projection	IEA
GO:0043162	Process	Ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway	IMP	21757351
GO:0043328	Process	Protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway	IBA
GO:0045022	Process	Early endosome to late endosome transport	IBA
GO:0045022	Process	Early endosome to late endosome transport	IMP	24821423
GO:0060271	Process	Cilium assembly	IMP	20393563
GO:0061357	Process	Positive regulation of Wnt protein secretion	IMP	24821423
GO:0070062	Component	Extracellular exosome	HDA	19056867
GO:1903387	Process	Positive regulation of homophilic cell adhesion	IMP	21724833
GO:1903393	Process	Positive regulation of adherens junction organization	IMP	21724833
GO:2000643	Process	Positive regulation of early endosome to late endosome transport	IMP	21724833

MIM	HGNC	e!Ensembl
606584	14406	ENSG00000076201

Protein

UniProt ID

Q9H3S7

Protein name

Tyrosine-protein phosphatase non-receptor type 23 (EC 3.1.3.48) (His domain-containing protein tyrosine phosphatase) (HD-PTP) (Protein tyrosine phosphatase TD14) (PTP-TD14)

Protein function

Plays a role in sorting of endocytic ubiquitinated cargos into multivesicular bodies (MVBs) via its interaction with the ESCRT-I complex (endosomal sorting complex required for transport I), and possibly also other ESCRT complexes (PubMed:184345

PDB

3RAU , 5CRU , 5CRV , 5LM1 , 5LM2 , 5MJY , 5MJZ , 5MK0 , 5MK1 , 5MK2 , 5MK3

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF03097	BRO1	9 → 380	BRO1-like domain	Domain
PF13949	ALIX_LYPXL_bnd	416 → 702	ALIX V-shaped domain binding to HIV	Domain
PF00102	Y_phosphatase	1217 → 1451	Protein-tyrosine phosphatase	Domain

Sequence

MEAVPRMPMIWLDLKEAGDFHFQPAVKKFVLKNYGENPEAYNEELKKLELLRQNAVRVPR
DFEGCSVLRKYLGQLHYLQSRVPMGSGQEAAVPVTWTEIFSGKSVAHEDIKYEQACILYN
LGALHSMLGAMDKRVSEEGMKVSCTHFQCAAGAFAYLREHFPQAYSVDMSRQILTLNVNL
MLGQAQECLLEKSMLDNRKSFLVARISAQVVDYYKEACRALENPDTASLLGRIQKDWKKL
VQMKIYYFAAVAHLHMGKQAEEQQKFGERVAYFQSALDKLNEAIKLAKGQPDTVQDALRF
TMDVIGGKYNSAKKDNDFIYHEAVPALDTLQPVKGAPLVKPLPVNPTDPAVTGPDIFAKL
VPMAAHEASSLYSEEKAKLLREMMAKIEDKNEVLDQFMDSMQLDPETVDNLDAYSHIPPQ
LMEKCAALSVRPDTVRNLVQSMQVLSGVFTDVEASLKDIRDLLEEDELLEQKFQEAVGQA
GAISITSKAELAEVRREWAKYMEVHEKASFTNSELHRAMNLHVGNLRLLSGPLDQVRAAL
PTPALSPEDKAVLQNLKRILAKVQEMRDQRVSLEQQLRELIQKDDITASLVTTDHSEMKK
LFEEQLKKYDQLKVYLEQNLAAQDRVLCALTEANVQYAAVRRVLSDLDQKWNSTLQTLVA
SYEAYEDLMKKSQEGRDFYADLESKVAALLERTQSTCQAREAARQQLLDRELKKKPPPRP
TAPKPLLPRREESEAVEAGDPPEELRSLPPDMVAGPRLPDTFLGSATPLHFPPSPFPSST
GPGPHYLSGPLPPGTYSGPTQLIQPRAPGPHAMPVAPGPALYPAPAYTPELGLVPRSSPQ
HGVVSSPYVGVGPAPPVAGLPSAPPPQFSGPELAMAVRPATTTVDSIQAPIPSHTAPRPN
PTPAPPPPCFPVPPPQPLPTPYTYPAGAKQPIPAQHHFSSGIPAGFPAPRIGPQPQPHPQ
PHPSQAFGPQPPQQPLPLQHPHLFPPQAPGLLPPQSPYPYAPQPGVLGQPPPPLHTQLYP
GPAQDPLPAHSGALPFPSPGPPQPPHPPLAYGPAPSTRPMGPQAAPLTIRGPSSAGQSTP
SPHLVPSPAPSPGPGPVPPRPPAAEPPPCLRRGAAAADLLSSSPESQHGGTQSPGGGQPL
LQPTKVDAAEGRRPQALRLIERDPYEHPERLRQLQQELEAFRGQLGDVGALDTVWRELQD
AQEHDARGRSIAIARCYSLKNRHQDVMPYDSNRVVLRSGKDDYINASCVEGLSPYCPPLV
ATQAPLPGTAADFWLMVHEQKVSVIVMLVSEAEMEKQKVARYFPTERGQPMVHGALSLAL
SSVRSTETHVERVLSLQFRDQSLKRSLVHLHFPTWPELGLPDSPSNLLRFIQEVHAHYLH
QRPLHTPIIVHCSSGVGRTGAFALLYAAVQEVEAGNGIPELPQLVRRMRQQRKHMLQEKL
HLRFCYEAVVRHVEQVLQRHGVPPPCKPLASASISQKNHLPQDSQDLVLGGDVPISSIQA
TIAKLSIRPPGGLESPVASLPGPAEPPGLPPASLPESTPIPSSSPPPLSSPLPEAPQPKE
EPPVPEAPSSGPPSSSLELLASLTPEAFSLDSSLRGKQRMSKHNFLQAHNGQGLRATRPS
DDPLSLLDPLWTLNKT

Sequence length

1636

Interactions

View interactions

	Reactome
			Interleukin-37 signaling

Show/Hide Unknown Diseases (5)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Breast Cancer	Breast cancer	N/A	N/A	GWAS
Colorectal Cancer	Colorectal cancer	N/A	N/A	GWAS
Developmental Delay	global developmental delay	N/A	N/A	ClinVar
Diabetes	Type 2 diabetes (adjusted for BMI)	N/A	N/A	GWAS
Gout	Gout	N/A	N/A	GWAS

Show/Hide Text Mining Associations (22)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Blindness Cortical	Associate	29899372
Brain Diseases	Associate	31395947
Breast Neoplasms	Associate	21724833
Carcinoma Non Small Cell Lung	Associate	37821451
Demyelinating Diseases	Associate	29899372
Developmental Disabilities	Associate	29899372, 31395947
Embryo Loss	Associate	31395947
Epilepsy	Associate	29899372
Epileptic Encephalopathy Early Infantile 3	Associate	29899372, 31957018
Genetic Diseases Inborn	Associate	31395947
Hydrocephalus	Associate	31395947
Hypersensitivity Delayed	Associate	31395947
Intellectual Disability	Associate	31395947
Language Disorders	Associate	31395947
Lung Neoplasms	Inhibit	37821451
Microcephaly	Associate	31395947
Microphthalmia Syndromic 10	Associate	29899372, 31395947
Muscle Spasticity	Associate	31395947
Neoplasms	Inhibit	19340315
Neoplasms	Associate	21724833
Optic Atrophy	Associate	31395947
Seizures	Associate	31395947

PTPN23 (protein tyrosine phosphatase non-receptor type 23)