Seroatlas · Human Serome Atlas

PCDH12

Protocadherin-12

Also known as: PCD12_HUMAN

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

Protein identityUniProt · HPA

UniProt accession: Q9NPG4
Gene: PCDH12
Ensembl: ENSG00000113555
Chromosome: 5
Canonical length: 1184 aa
Protein class: Disease related genes, Human disease related genes, Plasma proteins, Predicted membrane proteins, Predicted secreted proteins
Secretome location: Secreted to blood

OverviewNCBI Gene

This gene belongs to the protocadherin gene family, a subfamily of the cadherin superfamily. The encoded protein consists of an extracellular domain containing 6 cadherin repeats, a transmembrane domain and a cytoplasmic tail that differs from those of the classical cadherins. The gene localizes to the region on chromosome 5 where the protocadherin gene clusters reside. The exon organization of this transcript is similar to that of the gene cluster transcripts, notably the first large exon, but no significant sequence homology exists. The function of this cellular adhesion protein is undetermined but mouse protocadherin 12 does not bind catenins and appears to have no affect on cell migration or growth. [provided by RefSeq, Jul 2008]

Canonical amino-acid sequenceUniProt

1184 residues, UniProt reviewed canonical sequence.

>Q9NPG4|PCDH12
     1  MMQLLQLLLG LLGPGGYLFL LGDCQEVTTL TVKYQVSEEV PSGTVIGKLS QELGREERRR
    61  QAGAAFQVLQ LPQALPIQVD SEEGLLSTGR RLDREQLCRQ WDPCLVSFDV LATGDLALIH
   121  VEIQVLDIND HQPRFPKGEQ ELEISESASL RTRIPLDRAL DPDTGPNTLH TYTLSPSEHF
   181  ALDVIVGPDE TKHAELIVVK ELDREIHSFF DLVLTAYDNG NPPKSGTSLV KVNVLDSNDN
   241  SPAFAESSLA LEIQEDAAPG TLLIKLTATD PDQGPNGEVE FFLSKHMPPE VLDTFSIDAK
   301  TGQVILRRPL DYEKNPAYEV DVQARDLGPN PIPAHCKVLI KVLDVNDNIP SIHVTWASQP
   361  SLVSEALPKD SFIALVMADD LDSGHNGLVH CWLSQELGHF RLKRTNGNTY MLLTNATLDR
   421  EQWPKYTLTL LAQDQGLQPL SAKKQLSIQI SDINDNAPVF EKSRYEVSTR ENNLPSLHLI
   481  TIKAHDADLG INGKVSYRIQ DSPVAHLVAI DSNTGEVTAQ RSLNYEEMAG FEFQVIAEDS
   541  GQPMLASSVS VWVSLLDAND NAPEVVQPVL SDGKASLSVL VNASTGHLLV PIETPNGLGP
   601  AGTDTPPLAT HSSRPFLLTT IVARDADSGA NGEPLYSIRS GNEAHLFILN PHTGQLFVNV
   661  TNASSLIGSE WELEIVVEDQ GSPPLQTRAL LRVMFVTSVD HLRDSARKPG ALSMSMLTVI
   721  CLAVLLGIFG LILALFMSIC RTEKKDNRAY NCREAESTYR QQPKRPQKHI QKADIHLVPV
   781  LRGQAGEPCE VGQSHKDVDK EAMMEAGWDP CLQAPFHLTP TLYRTLRNQG NQGAPAESRE
   841  VLQDTVNLLF NHPRQRNASR ENLNLPEPQP ATGQPRSRPL KVAGSPTGRL AGDQGSEEAP
   901  QRPPASSATL RRQRHLNGKV SPEKESGPRQ ILRSLVRLSV AAFAERNPVE ELTVDSPPVQ
   961  QISQLLSLLH QGQFQPKPNH RGNKYLAKPG GSRSAIPDTD GPSARAGGQT DPEQEEGPLD
  1021  PEEDLSVKQL LEEELSSLLD PSTGLALDRL SAPDPAWMAR LSLPLTTNYR DNVISPDAAA
  1081  TEEPRTFQTF GKAEAPELSP TGTRLASTFV SEMSSLLEML LEQRSSMPVE AASEALRRLS
  1141  VCGRTLSLDL ATSAASGMKV QGDPGGKTGT EGKSRGSSSS SRCL

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against PCDH12 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: Cell surface
Secreted: No
Transmembrane segments: 1
Mean surface accessibility (rSASA): 0.47
Highest tissue expression: 28 nTPM

Expression across tissuesHPA

Tissue

placenta: 28 nTPM
spleen: 18 nTPM
lung: 15 nTPM
adipose tissue: 13 nTPM
heart muscle: 13 nTPM
thyroid gland: 7.2 nTPM

Single-cell type

cardiomyocytes: 119 nCPM
epicardial cells: 84 nCPM
hofbauer cells: 84 nCPM
lymphatic endothelial cells: 40 nCPM
vascular endothelial cells: 33 nCPM
kupffer cells: 28 nCPM

Immune cell

non-classical monocyte: 4.7 nTPM
intermediate monocyte: 0.5 nTPM
classical monocyte: 0.3 nTPM
myeloid DC: 0.1 nTPM
total PBMC: 0.1 nTPM
basophil: 0 nTPM

Brain region

cerebellum: 9 nTPM
cerebral cortex: 7.2 nTPM
thalamus: 6.6 nTPM
choroid plexus: 6.2 nTPM
basal ganglia: 5.7 nTPM
hypothalamus: 5.5 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about PCDH12.

Disease | AllUniProt

Conditions PCDH12 is implicated in, by any mechanism.

Diencephalic-mesencephalic junction dysplasia syndrome 1 (DMJDS1) MIM:251280

Disease | GeneticClinVar

30 pathogenic / likely-pathogenic of 512 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

Diencephalic-mesencephalic junction dysplasia syndrome 1
Diencephalic-mesencephalic junction dysplasia
Cerebellar ataxia
Abnormal facial shape
Coats disease

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): 0.98
gnomAD pLI: 0
gnomAD missense Z: 0.78
DepMap mean gene effect: 0.03
DepMap dependency class: none

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

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads PCDH12 as an antibody target. Whether an autoantibody or antibody against PCDH12 could matter depends on whether native PCDH12 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

PCDH12 is annotated at the cell surface, where native PCDH12 is exposed to circulating antibodies and is a prime autoantibody target that could block, deplete, or overstimulate it.

Annotation status

The present source text does not explicitly label PCDH12 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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