Seroatlas · Human Serome Atlas

PTPN23

Tyrosine-protein phosphatase non-receptor type 23

Also known as: DKFZP564F0923, HD-PTP, KIAA1471, PTN23_HUMAN

Cross-references: UniProt · Ensembl · Human Protein Atlas · GeneCards · NCBI Gene

Protein identityUniProt · HPA

UniProt accession: Q9H3S7
Gene: PTPN23
Ensembl: ENSG00000076201
Chromosome: 3
Canonical length: 1636 aa
Protein class: Disease related genes, Enzymes, Human disease related genes, Potential drug targets, Predicted intracellular proteins
Subcellular location: Nucleoplasm,Nuclear bodies,Vesicles,Centriolar satellite,Basal body,Cytosol,Calyx,Mid piece

OverviewNCBI 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) 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]

Canonical amino-acid sequenceUniProt

1636 residues, UniProt reviewed canonical sequence.

>Q9H3S7|PTPN23
     1  MEAVPRMPMI WLDLKEAGDF HFQPAVKKFV LKNYGENPEA YNEELKKLEL LRQNAVRVPR
    61  DFEGCSVLRK YLGQLHYLQS RVPMGSGQEA AVPVTWTEIF SGKSVAHEDI KYEQACILYN
   121  LGALHSMLGA MDKRVSEEGM KVSCTHFQCA AGAFAYLREH FPQAYSVDMS RQILTLNVNL
   181  MLGQAQECLL EKSMLDNRKS FLVARISAQV VDYYKEACRA LENPDTASLL GRIQKDWKKL
   241  VQMKIYYFAA VAHLHMGKQA EEQQKFGERV AYFQSALDKL NEAIKLAKGQ PDTVQDALRF
   301  TMDVIGGKYN SAKKDNDFIY HEAVPALDTL QPVKGAPLVK PLPVNPTDPA VTGPDIFAKL
   361  VPMAAHEASS LYSEEKAKLL REMMAKIEDK NEVLDQFMDS MQLDPETVDN LDAYSHIPPQ
   421  LMEKCAALSV RPDTVRNLVQ SMQVLSGVFT DVEASLKDIR DLLEEDELLE QKFQEAVGQA
   481  GAISITSKAE LAEVRREWAK YMEVHEKASF TNSELHRAMN LHVGNLRLLS GPLDQVRAAL
   541  PTPALSPEDK AVLQNLKRIL AKVQEMRDQR VSLEQQLREL IQKDDITASL VTTDHSEMKK
   601  LFEEQLKKYD QLKVYLEQNL AAQDRVLCAL TEANVQYAAV RRVLSDLDQK WNSTLQTLVA
   661  SYEAYEDLMK KSQEGRDFYA DLESKVAALL ERTQSTCQAR EAARQQLLDR ELKKKPPPRP
   721  TAPKPLLPRR EESEAVEAGD PPEELRSLPP DMVAGPRLPD TFLGSATPLH FPPSPFPSST
   781  GPGPHYLSGP LPPGTYSGPT QLIQPRAPGP HAMPVAPGPA LYPAPAYTPE LGLVPRSSPQ
   841  HGVVSSPYVG VGPAPPVAGL PSAPPPQFSG PELAMAVRPA TTTVDSIQAP IPSHTAPRPN
   901  PTPAPPPPCF PVPPPQPLPT PYTYPAGAKQ PIPAQHHFSS GIPAGFPAPR IGPQPQPHPQ
   961  PHPSQAFGPQ PPQQPLPLQH PHLFPPQAPG LLPPQSPYPY APQPGVLGQP PPPLHTQLYP
  1021  GPAQDPLPAH SGALPFPSPG PPQPPHPPLA YGPAPSTRPM GPQAAPLTIR GPSSAGQSTP
  1081  SPHLVPSPAP SPGPGPVPPR PPAAEPPPCL RRGAAAADLL SSSPESQHGG TQSPGGGQPL
  1141  LQPTKVDAAE GRRPQALRLI ERDPYEHPER LRQLQQELEA FRGQLGDVGA LDTVWRELQD
  1201  AQEHDARGRS IAIARCYSLK NRHQDVMPYD SNRVVLRSGK DDYINASCVE GLSPYCPPLV
  1261  ATQAPLPGTA ADFWLMVHEQ KVSVIVMLVS EAEMEKQKVA RYFPTERGQP MVHGALSLAL
  1321  SSVRSTETHV ERVLSLQFRD QSLKRSLVHL HFPTWPELGL PDSPSNLLRF IQEVHAHYLH
  1381  QRPLHTPIIV HCSSGVGRTG AFALLYAAVQ EVEAGNGIPE LPQLVRRMRQ QRKHMLQEKL
  1441  HLRFCYEAVV RHVEQVLQRH GVPPPCKPLA SASISQKNHL PQDSQDLVLG GDVPISSIQA
  1501  TIAKLSIRPP GGLESPVASL PGPAEPPGLP PASLPESTPI PSSSPPPLSS PLPEAPQPKE
  1561  EPPVPEAPSS GPPSSSLELL ASLTPEAFSL DSSLRGKQRM SKHNFLQAHN GQGLRATRPS
  1621  DDPLSLLDPL WTLNKT

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against PTPN23 can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.

Antibody reachability: Intracellular
Secreted: No
Transmembrane segments: 0
Mean surface accessibility (rSASA): 0.43
Highest tissue expression: 26 nTPM

Expression across tissuesHPA

Tissue

skeletal muscle: 26 nTPM
pituitary gland: 24 nTPM
thyroid gland: 22 nTPM
skin: 22 nTPM
parathyroid gland: 21 nTPM
cerebellum: 19 nTPM

Single-cell type

alveolar cells type 1: 45 nCPM
epicardial cells: 36 nCPM
cone photoreceptor cells: 35 nCPM
endometrial glandular cells: 31 nCPM
respiratory ionocytes: 28 nCPM
somatotrophs: 26 nCPM

Immune cell

basophil: 0.4 nTPM
T-reg: 0.4 nTPM
memory B-cell: 0.3 nTPM
total PBMC: 0.3 nTPM
memory CD8 T-cell: 0.2 nTPM
NK-cell: 0.2 nTPM

Brain region

white matter: 40 nTPM
basal ganglia: 33 nTPM
medulla oblongata: 32 nTPM
cerebral cortex: 32 nTPM
pons: 30 nTPM
midbrain: 29 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about PTPN23.

Disease | AllUniProt

Conditions PTPN23 is implicated in, by any mechanism.

Neurodevelopmental disorder and structural brain anomalies with or without seizures and spasticity (NEDBASS) MIM:618890

Disease | GeneticClinVar

53 pathogenic / likely-pathogenic of 1,605 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

Neurodevelopmental disorder and structural brain anomalies with or without seizures and spasticity
Brain atrophy
Global developmental delay
Seizure
Hereditary spastic paraplegia

Genetic constraint and essentialitygnomAD · DepMap

Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.

gnomAD LOEUF (loss-of-function intolerance): 0.37
gnomAD pLI: 0.03
gnomAD missense Z: 1.33
DepMap mean gene effect: -1.01
DepMap dependency class: common

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 4% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

Molecular functions

Cellular components

Protein domainsUniProt · Pfam · InterPro

KeywordsUniProt

InteractionsUniProt · HPA

Protein binding partners of PTPN23 in the human serome: UniProt-annotated complex subunits plus reported interactors. Each links to its own Seroatlas record.

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads PTPN23 as an antibody target. Whether an autoantibody or antibody against PTPN23 could matter depends on whether native PTPN23 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

PTPN23 is annotated as predominantly intracellular. Intracellular proteins are common autoantibody markers, becoming visible to the immune system after cell injury or altered processing, but are usually markers of disease rather than direct drivers.

Annotation status

The present source text does not explicitly label PTPN23 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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