Seroatlas · Human Serome Atlas

PCDHA6

Protocadherin alpha-6

Also known as: CNR2, CNRS2, CRNR2, PCDA6_HUMAN, PCDH-ALPHA6

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

Protein identityUniProt · HPA

UniProt accession
Q9UN73
Gene
PCDHA6
Ensembl
ENSG00000081842
Chromosome
5
Canonical length
950 aa
Protein class
Predicted membrane proteins, Predicted secreted proteins
Subcellular location
Vesicles
Secretome location
Secreted in brain

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

950 residues, UniProt reviewed canonical sequence.

>Q9UN73|PCDHA6
     1  MVFTPEDRLG KQCLLLPLLL LAAWKVGSGQ LHYSVPEEAK HGTFVGRIAQ DLGLELAELV
    61  PRLFRMASKD REDLLEVNLQ NGILFVNSRI DREELCGRSA ECSIHLEVIV DRPLQVFHVD
   121  VEVRDINDNP PLFPVEEQRV LIYESRLPDS VFPLEGASDA DVGSNSILTY KLSSSEYFGL
   181  DVKINSDDNK QIGLLLKKSL DREEAPAHNL FLTATDGGKP ELTGTVQLLV TVLDVNDNAP
   241  TFEQSEYEVR IFENADNGTT VIRLNASDRD EGANGAISYS FNSLVAAMVI DHFSIDRNTG
   301  EIVIRGNLDF EQENLYKILI DATDKGHPPM AGHCTVLVRI LDKNDNVPEI ALTSLSLPVR
   361  EDAQFGTVIA LISVNDLDSG ANGQVNCSLT PHVPFKLVST FKNYYSLVLD SALDRESVSA
   421  YELVVTARDG GSPSLWATAS LSVEVADMND NAPAFAQPEY TVFVKENNPP GCHIFTVSAR
   481  DADAQENALV SYSLVERRVG ERALSSYISV HAESGKVYAL QPLDHEELEL LQFQVSARDA
   541  GVPPLGSNVT LQVFVLDEND NAPALLAPRV GGTGGAVSEL VPRSLGAGQV VAKVRAVDAD
   601  SGYNAWLSYE LQPPASSARF PFRVGLYTGE ISTTRVLDEA DSPRHRLLVL VKDHGEPALT
   661  ATATVLVSLV ESGQAPKASS RASVGAAGPE AALVDVNVYL IIAICAVSSL LVLTLLLYTA
   721  LRCSAPPTEG ACTADKPTLV CSSAVGSWSY SQQRRQRVCS GEGPPKMDLM AFSPSLSPCP
   781  IMMGKAENQD LNEDHDAKPR QPNPDWRYSA SLRAGMHSSV HLEEAGILRA GPGGPDQQWP
   841  TVSSATPEPE AGEVSPPVGA GVNSNSWTFK YGPGNPKQSG PGELPDKFII PGSPAIISIR
   901  QEPTNSQIDK SDFITFGKKE ETKKKKKKKK GNKTQEKKEK GNSTTDNSDQ

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against PCDHA6 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
2.4 nTPM

Expression across tissuesHPA

Tissue

  • cerebellum: 2.4 nTPM
  • cerebral cortex: 2.4 nTPM
  • parathyroid gland: 1.4 nTPM
  • pituitary gland: 1.1 nTPM
  • retina: 1 nTPM
  • spinal cord: 1 nTPM

Single-cell type

  • oligodendrocyte progenitor cells: 66 nCPM
  • bergmann glia: 46 nCPM
  • brain inhibitory neurons: 36 nCPM
  • brain excitatory neurons: 34 nCPM
  • other brain neurons: 21 nCPM
  • ependymal cells: 16 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: 14 nTPM
  • cerebral cortex: 7.7 nTPM
  • basal ganglia: 7.3 nTPM
  • white matter: 7.3 nTPM
  • hypothalamus: 7.1 nTPM
  • hippocampal formation: 6.4 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)
1.07
gnomAD pLI
0
gnomAD missense Z
-1.01
DepMap mean gene effect
-0.06
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

KeywordsUniProt

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads PCDHA6 as an antibody target. Whether an autoantibody or antibody against PCDHA6 could matter depends on whether native PCDHA6 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

PCDHA6 is annotated at the cell surface, where native PCDHA6 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 PCDHA6 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

Canonical record: https://seroatlas.com/gene/PCDHA6. Study-independent annotations aggregated from UniProt, Human Protein Atlas, PubMed, IEDB, Pfam, InterPro, Gene Ontology, AlphaFold, gnomAD, DepMap, ClinVar, TCGA. Catalog release seroatlas-reviewed-human-uniprot-20260313.

Seroatlas is the reference for exploring autoantibody and antibody serology at the human-protein level: the autoreactome and human serome, multiplex serology (HuProt, HuScan, VirScan, PhIP-Seq).

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