Seroatlas · Human Serome Atlas

PTPN13

Tyrosine-protein phosphatase non-receptor type 13

Also known as: PTN13_HUMAN, PTP-BAS, PTP-BL, PTP1E, PTPL1

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

Protein identityUniProt · HPA

UniProt accession: Q12923
Gene: PTPN13
Ensembl: ENSG00000163629
Chromosome: 4
Canonical length: 2485 aa
Protein class: Cancer-related genes, Enzymes, Predicted intracellular proteins
Subcellular location: Plasma membrane,Primary cilium,Primary cilium transition zone,Basal body,Cytosol

OverviewNCBI Gene

The protein encoded by this gene is a member of the protein tyrosine phosphatase (PTP) family. PTPs are signaling molecules that regulate a variety of cellular processes including cell growth, differentiation, mitotic cycle, and oncogenic transformation. This PTP is a large intracellular protein. It has a catalytic PTP domain at its C-terminus and two major structural domains: a region with five PDZ domains and a FERM domain that binds to plasma membrane and cytoskeletal elements. This PTP was found to interact with, and dephosphorylate, Fas receptor and IkappaBalpha through the PDZ domains. This suggests it has a role in Fas mediated programmed cell death. This PTP was also shown to interact with GTPase-activating protein, and thus may function as a regulator of Rho signaling pathways. Four alternatively spliced transcript variants, which encode distinct proteins, have been reported. [provided by RefSeq, Oct 2008]

Canonical amino-acid sequenceUniProt

2485 residues, UniProt reviewed canonical sequence.

>Q12923|PTPN13
     1  MHVSLAEALE VRGGPLQEEE IWAVLNQSAE SLQELFRKVS LADPAALGFI ISPWSLLLLP
    61  SGSVSFTDEN ISNQDLRAFT APEVLQNQSL TSLSDVEKIH IYSLGMTLYW GADYEVPQSQ
   121  PIKLGDHLNS ILLGMCEDVI YARVSVRTVL DACSAHIRNS NCAPSFSYVK HLVKLVLGNL
   181  SGTDQLSCNS EQKPDRSQAI RDRLRGKGLP TGRSSTSDVL DIQKPPLSHQ TFLNKGLSKS
   241  MGFLSIKDTQ DENYFKDILS DNSGREDSEN TFSPYQFKTS GPEKKPIPGI DVLSKKKIWA
   301  SSMDLLCTAD RDFSSGETAT YRRCHPEAVT VRTSTTPRKK EARYSDGSIA LDIFGPQKMD
   361  PIYHTRELPT SSAISSALDR IRERQKKLQV LREAMNVEEP VRRYKTYHGD VFSTSSESPS
   421  IISSESDFRQ VRRSEASKRF ESSSGLPGVD ETLSQGQSQR PSRQYETPFE GNLINQEIML
   481  KRQEEELMQL QAKMALRQSR LSLYPGDTIK ASMLDITRDP LREIALETAM TQRKLRNFFG
   541  PEFVKMTIEP FISLDLPRSI LTKKGKNEDN RRKVNIMLLN GQRLELTCDT KTICKDVFDM
   601  VVAHIGLVEH HLFALATLKD NEYFFVDPDL KLTKVAPEGW KEEPKKKTKA TVNFTLFFRI
   661  KFFMDDVSLI QHTLTCHQYY LQLRKDILEE RMHCDDETSL LLASLALQAE YGDYQPEVHG
   721  VSYFRMEHYL PARVMEKLDL SYIKEELPKL HNTYVGASEK ETELEFLKVC QRLTEYGVHF
   781  HRVHPEKKSQ TGILLGVCSK GVLVFEVHNG VRTLVLRFPW RETKKISFSK KKITLQNTSD
   841  GIKHGFQTDN SKICQYLLHL CSYQHKFQLQ MRARQSNQDA QDIERASFRS LNLQAESVRG
   901  FNMGRAISTG SLASSTLNKL AVRPLSVQAE ILKRLSCSEL SLYQPLQNSS KEKNDKASWE
   961  EKPREMSKSY HDLSQASLYP HRKNVIVNME PPPQTVAELV GKPSHQMSRS DAESLAGVTK
  1021  LNNSKSVASL NRSPERRKHE SDSSSIEDPG QAYVLGMTMH SSGNSSSQVP LKENDVLHKR
  1081  WSIVSSPERE ITLVNLKKDA KYGLGFQIIG GEKMGRLDLG IFISSVAPGG PADLDGCLKP
  1141  GDRLISVNSV SLEGVSHHAA IEILQNAPED VTLVISQPKE KISKVPSTPV HLTNEMKNYM
  1201  KKSSYMQDSA IDSSSKDHHW SRGTLRHISE NSFGPSGGLR EGSLSSQDSR TESASLSQSQ
  1261  VNGFFASHLG DQTWQESQHG SPSPSVISKA TEKETFTDSN QSKTKKPGIS DVTDYSDRGD
  1321  SDMDEATYSS SQDHQTPKQE SSSSVNTSNK MNFKTFSSSP PKPGDIFEVE LAKNDNSLGI
  1381  SVTGGVNTSV RHGGIYVKAV IPQGAAESDG RIHKGDRVLA VNGVSLEGAT HKQAVETLRN
  1441  TGQVVHLLLE KGQSPTSKEH VPVTPQCTLS DQNAQGQGPE KVKKTTQVKD YSFVTEENTF
  1501  EVKLFKNSSG LGFSFSREDN LIPEQINASI VRVKKLFPGQ PAAESGKIDV GDVILKVNGA
  1561  SLKGLSQQEV ISALRGTAPE VFLLLCRPPP GVLPEIDTAL LTPLQSPAQV LPNSSKDSSQ
  1621  PSCVEQSTSS DENEMSDKSK KQCKSPSRRD SYSDSSGSGE DDLVTAPANI SNSTWSSALH
  1681  QTLSNMVSQA QSHHEAPKSQ EDTICTMFYY PQKIPNKPEF EDSNPSPLPP DMAPGQSYQP
  1741  QSESASSSSM DKYHIHHISE PTRQENWTPL KNDLENHLED FELEVELLIT LIKSEKGSLG
  1801  FTVTKGNQRI GCYVHDVIQD PAKSDGRLKP GDRLIKVNDT DVTNMTHTDA VNLLRAASKT
  1861  VRLVIGRVLE LPRIPMLPHL LPDITLTCNK EELGFSLCGG HDSLYQVVYI SDINPRSVAA
  1921  IEGNLQLLDV IHYVNGVSTQ GMTLEEVNRA LDMSLPSLVL KATRNDLPVV PSSKRSAVSA
  1981  PKSTKGNGSY SVGSCSQPAL TPNDSFSTVA GEEINEISYP KGKCSTYQIK GSPNLTLPKE
  2041  SYIQEDDIYD DSQEAEVIQS LLDVVDEEAQ NLLNENNAAG YSCGPGTLKM NGKLSEERTE
  2101  DTDCDGSPLP EYFTEATKMN GCEEYCEEKV KSESLIQKPQ EKKTDDDEIT WGNDELPIER
  2161  TNHEDSDKDH SFLTNDELAV LPVVKVLPSG KYTGANLKSV IRVLRGLLDQ GIPSKELENL
  2221  QELKPLDQCL IGQTKENRRK NRYKNILPYD ATRVPLGDEG GYINASFIKI PVGKEEFVYI
  2281  ACQGPLPTTV GDFWQMIWEQ KSTVIAMMTQ EVEGEKIKCQ RYWPNILGKT TMVSNRLRLA
  2341  LVRMQQLKGF VVRAMTLEDI QTREVRHISH LNFTAWPDHD TPSQPDDLLT FISYMRHIHR
  2401  SGPIITHCSA GIGRSGTLIC IDVVLGLISQ DLDFDISDLV RCMRLQRHGM VQTEDQYIFC
  2461  YQVILYVLTR LQAEEEQKQQ PQLLK

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against PTPN13 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): 0.44
Highest tissue expression: 115 nTPM

Expression across tissuesHPA

Tissue

retina: 115 nTPM
skin: 53 nTPM
kidney: 25 nTPM
epididymis: 24 nTPM
vagina: 22 nTPM
lung: 22 nTPM

Single-cell type

podocytes: 1,755 nCPM
rod photoreceptor cells: 1,490 nCPM
ocular epithelial cells: 1,474 nCPM
retinal pigment epithelial cells: 1,381 nCPM
cone photoreceptor cells: 878 nCPM
renal connecting tubule cells: 786 nCPM

Immune cell

non-classical monocyte: 2 nTPM
intermediate monocyte: 1.3 nTPM
MAIT T-cell: 0.9 nTPM
memory CD4 T-cell: 0.8 nTPM
myeloid DC: 0.2 nTPM
classical monocyte: 0.1 nTPM

Brain region

choroid plexus: 60 nTPM
white matter: 54 nTPM
medulla oblongata: 49 nTPM
basal ganglia: 47 nTPM
hippocampal formation: 42 nTPM
thalamus: 41 nTPM

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): 0.64
gnomAD pLI: 0
gnomAD missense Z: 0.58
DepMap mean gene effect: 0.03
DepMap dependency class: selective

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

Tyrosine-specific protein phosphatase, PTPase domain
FERM domain
Tyrosine-specific protein phosphatases domain
PDZ domain
Protein-tyrosine phosphatase, catalytic
KIND domain
PH-like domain superfamily
FERM/acyl-CoA-binding protein superfamily
FERM, N-terminal
FERM, C-terminal PH-like domain
FERM central domain
Band 4.1 domain
Protein-tyrosine phosphatase-like
Ubiquitin-like domain superfamily
FERM superfamily, second domain
PDZ superfamily
Non-receptor Tyrosine-protein Phosphatases
Protein-tyrosine phosphatase
FERM central domain
PDZ domain
FERM N-terminal domain
FERM C-terminal PH-like domain
Tyrosine-protein phosphatase non-receptor type 13
Unstructured linker region on PTN13 protein between PDZ

KeywordsUniProt

InteractionsUniProt · HPA

Protein binding partners of PTPN13 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 PTPN13 as an antibody target. Whether an autoantibody or antibody against PTPN13 could matter depends on whether native PTPN13 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

PTPN13 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 PTPN13 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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