Seroatlas · Human Serome Atlas

PCDHA12

Protocadherin alpha-12

Also known as: PCDAC_HUMAN, PCDH-ALPHA12

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

Protein identityUniProt · HPA

UniProt accession: Q9UN75
Gene: PCDHA12
Ensembl: ENSG00000251664
Chromosome: 5
Canonical length: 941 aa
Protein class: Predicted membrane proteins
Subcellular location: Plasma membrane,Cytosol

OverviewNCBI Gene

This gene is a member of the protocadherin alpha gene cluster, one of three related gene clusters tandemly linked on chromosome five that demonstrate an unusual genomic organization similar to that of B-cell and T-cell receptor gene clusters. The alpha gene cluster is composed of 15 cadherin superfamily genes related to the mouse CNR genes and consists of 13 highly similar and 2 more distantly related coding sequences. The tandem array of 15 N-terminal exons, or variable exons, are followed by downstream C-terminal exons, or constant exons, which are shared by all genes in the cluster. The large, uninterrupted N-terminal exons each encode six cadherin ectodomains while the C-terminal exons encode the cytoplasmic domain. These neural cadherin-like cell adhesion proteins are integral plasma membrane proteins that most likely play a critical role in the establishment and function of specific cell-cell connections in the brain. Alternative splicing has been observed and additional variants have been suggested but their full-length nature has yet to be determined. [provided by RefSeq, Jul 2008]

Canonical amino-acid sequenceUniProt

941 residues, UniProt reviewed canonical sequence.

>Q9UN75|PCDHA12
     1  MVIIGPRGPG SQRLLLSLLL LAAWEVGSGQ LHYSVYEEAK HGTFVGRIAQ DLGLELAELV
    61  PRLFRVASKR HGDLLEVNLQ NGILFVNSRI DREKLCGRSA ECSIHLEVIV DRPLQVFHVD
   121  VEVKDINDNP PVFREREQKV PVSESAPLDS HFPLEGASDA DIGVNSLLTY ALSLNENFEL
   181  KIKTKKDKSI LPELVLRKLL DREQTPKLNL LLMVIDGGKP ELTGSVQIQI TVLDVNDNGP
   241  AFDKPSYKVV LSENVQNDTR VIQLNASDPD EGLNGEISYG IKMILPVSEK CMFSINPDTG
   301  EIRIYGELDF EENNAYEIQV NAIDKGIPSM AGHSMVLVEV LDVNDNVPEV MVTSLSLPVQ
   361  EDAQVGTVIA LISVSDRDSG ANGQVICSLT PHVPFKLVST YKNYYSLVLD SALDRESVSA
   421  YELVVTARDG GSPSLWATAR VSVEVADVND NAPAFAQPEY TVFVKENNPP GCHIFTVSAW
   481  DADAQKNALV SYSLVERRVG EHALSSYVSV HAESGKVYAL QPLDHEELEL LQFQVSARDA
   541  GVPPLGSNVT LQVFVLDEND NAPALLATPA GSAGGAVSEL VPRSVGAGHV VAKVRAVDAD
   601  SGYNAWLSYE LQPAAVGAHI PFHVGLYTGE ISTTRILDEA DAPRHRLLVL VKDHGEPALT
   661  STATVLVSLV ENGQAPKTSS RASVGAVDPE AALVDINVYL IIAICAVSSL LVLTLLLYTA
   721  LRCSAPPTVS RCAPGKPTLV CSSAVGSWSY SQQRRQRVCS AESPPKTDLM AFSPSLQLSR
   781  EDCLNPPSEP RQPNPDWRYS ASLRAGMHSS VHLEEAGILR AGPGGPDQQW PTVSSATPEP
   841  EAGEVSPPVG AGVNSNSWTF KYGPGNPKQS GPGELPDKFI IPGSPAIISI RQEPTNSQID
   901  KSDFITFGKK EETKKKKKKK KGNKTQEKKE KGNSTTDNSD Q

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against PCDHA12 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): 0.44
Highest tissue expression: 1.6 nTPM

Expression across tissuesHPA

Tissue

cerebellum: 1.6 nTPM
lung: 1.4 nTPM
cerebral cortex: 0.8 nTPM
cervix: 0.8 nTPM
thyroid gland: 0.8 nTPM
gallbladder: 0.7 nTPM

Single-cell type

cholangiocytes: 2 nCPM
late spermatids: 1.6 nCPM
alveolar cells type 1: 1 nCPM
endometrial secretory cells: 1 nCPM
breast myoepithelial cells: 0.9 nCPM
late primary spermatocytes: 0.8 nCPM

Immune cell

basophil: 0 nTPM
classical monocyte: 0 nTPM
eosinophil: 0 nTPM
gdT-cell: 0 nTPM
intermediate monocyte: 0 nTPM
MAIT T-cell: 0 nTPM

Brain region

cerebellum: 11 nTPM
cerebral cortex: 4.5 nTPM
basal ganglia: 3.8 nTPM
white matter: 3.8 nTPM
pons: 3.5 nTPM
medulla oblongata: 3.4 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): 1.19
gnomAD pLI: 0
gnomAD missense Z: -0.34
DepMap mean gene effect: -0.09
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

plasma membrane

Protein domainsUniProt · Pfam · InterPro

KeywordsUniProt

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads PCDHA12 as an antibody target. Whether an autoantibody or antibody against PCDHA12 could matter depends on whether native PCDHA12 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

PCDHA12 is annotated at the cell surface, where native PCDHA12 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 PCDHA12 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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