Seroatlas · Human Serome Atlas

PCDH1

Protocadherin-1

Also known as: pc42, PCDH1_HUMAN

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

Protein identityUniProt · HPA

UniProt accession: Q08174
Gene: PCDH1
Ensembl: ENSG00000156453
Chromosome: 5
Canonical length: 1060 aa
Protein class: Plasma proteins, Predicted intracellular proteins, Predicted membrane proteins
Subcellular location: Nucleoplasm,Nucleoli,Cell Junctions

OverviewNCBI Gene

This gene belongs to the protocadherin subfamily within the cadherin superfamily. The encoded protein is a membrane protein found at cell-cell boundaries. It is involved in neural cell adhesion, suggesting a possible role in neuronal development. The protein includes an extracelllular region, containing 7 cadherin-like domains, a transmembrane region and a C-terminal cytoplasmic region. Cells expressing the protein showed cell aggregation activity. Alternative splicing occurs in this gene. [provided by RefSeq, Jul 2008]

Canonical amino-acid sequenceUniProt

1060 residues, UniProt reviewed canonical sequence.

>Q08174|PCDH1
     1  MDSGAGGRRC PEAALLILGP PRMEHLRHSP GPGGQRLLLP SMLLALLLLL APSPGHATRV
    61  VYKVPEEQPP NTLIGSLAAD YGFPDVGHLY KLEVGAPYLR VDGKTGDIFT TETSIDREGL
   121  RECQNQLPGD PCILEFEVSI TDLVQNGSPR LLEGQIEVQD INDNTPNFAS PVITLAIPEN
   181  TNIGSLFPIP LASDRDAGPN GVASYELQAG PEAQELFGLQ VAEDQEEKQP QLIVMGNLDR
   241  ERWDSYDLTI KVQDGGSPPR ASSALLRVTV LDTNDNAPKF ERPSYEAELS ENSPIGHSVI
   301  QVKANDSDQG ANAEIEYTFH QAPEVVRRLL RLDRNTGLIT VQGPVDREDL STLRFSVLAK
   361  DRGTNPKSAR AQVVVTVKDM NDNAPTIEIR GIGLVTHQDG MANISEDVAE ETAVALVQVS
   421  DRDEGENAAV TCVVAGDVPF QLRQASETGS DSKKKYFLQT TTPLDYEKVK DYTIEIVAVD
   481  SGNPPLSSTN SLKVQVVDVN DNAPVFTQSV TEVAFPENNK PGEVIAEITA SDADSGSNAE
   541  LVYSLEPEPA AKGLFTISPE TGEIQVKTSL DREQRESYEL KVVAADRGSP SLQGTATVLV
   601  NVLDCNDNDP KFMLSGYNFS VMENMPALSP VGMVTVIDGD KGENAQVQLS VEQDNGDFVI
   661  QNGTGTILSS LSFDREQQST YTFQLKAVDG GVPPRSAYVG VTINVLDEND NAPYITAPSN
   721  TSHKLLTPQT RLGETVSQVA AEDFDSGVNA ELIYSIAGGN PYGLFQIGSH SGAITLEKEI
   781  ERRHHGLHRL VVKVSDRGKP PRYGTALVHL YVNETLANRT LLETLLGHSL DTPLDIDIAG
   841  DPEYERSKQR GNILFGVVAG VVAVALLIAL AVLVRYCRQR EAKSGYQAGK KETKDLYAPK
   901  PSGKASKGNK SKGKKSKSPK PVKPVEDEDE AGLQKSLKFN LMSDAPGDSP RIHLPLNYPP
   961  GSPDLGRHYR SNSPLPSIQL QPQSPSASKK HQVVQDLPPA NTFVGTGDTT STGSEQYSDY
  1021  SYRTNPPKYP SKQVGQPFQL STPQPLPHPY HGAIWTEVWE

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against PCDH1 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): 0.4
Highest tissue expression: 40 nTPM

Expression across tissuesHPA

Tissue

esophagus: 40 nTPM
salivary gland: 27 nTPM
skin: 26 nTPM
lung: 26 nTPM
cerebral cortex: 23 nTPM
adipose tissue: 23 nTPM

Single-cell type

esophageal apical cells: 273 nCPM
salivary duct cells: 81 nCPM
foveolar cells: 66 nCPM
colonocytes: 58 nCPM
conjunctival goblet cells: 55 nCPM
vascular endothelial cells: 52 nCPM

Immune cell

gdT-cell: 0.3 nTPM
naive CD8 T-cell: 0.2 nTPM
memory CD8 T-cell: 0.1 nTPM
total PBMC: 0.1 nTPM
basophil: 0 nTPM
classical monocyte: 0 nTPM

Brain region

hippocampal formation: 91 nTPM
basal ganglia: 87 nTPM
cerebral cortex: 86 nTPM
amygdala: 78 nTPM
white matter: 65 nTPM
cerebellum: 61 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about PCDH1.

Disease | GeneticClinVar

1 pathogenic / likely-pathogenic of 158 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

Esophageal atresia/tracheoesophageal fistula

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): 0.24
gnomAD pLI: 1
gnomAD missense Z: 3.08
DepMap mean gene effect: 0.13
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 PCDH1 as an antibody target. Whether an autoantibody or antibody against PCDH1 could matter depends on whether native PCDH1 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

PCDH1 is annotated at the cell surface, where native PCDH1 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 PCDH1 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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