Seroatlas · Human Serome Atlas

PCDHB1

Protocadherin beta-1

Also known as: PCDB1_HUMAN, PCDH-BETA1

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

Protein identityUniProt · HPA

UniProt accession: Q9Y5F3
Gene: PCDHB1
Ensembl: ENSG00000171815
Chromosome: 5
Canonical length: 818 aa
Protein class: Predicted membrane proteins
Subcellular location: Nucleoplasm,Plasma membrane

OverviewNCBI Gene

This gene is a member of the protocadherin beta gene cluster, one of three related gene clusters tandemly linked on chromosome five. The gene clusters demonstrate an unusual genomic organization similar to that of B-cell and T-cell receptor gene clusters. The beta cluster contains 16 genes and 3 pseudogenes, each encoding 6 extracellular cadherin domains and a cytoplasmic tail that deviates from others in the cadherin superfamily. The extracellular domains interact in a homophilic manner to specify differential cell-cell connections. Unlike the alpha and gamma clusters, the transcripts from these genes are made up of only one large exon, not sharing common 3' exons as expected. These neural cadherin-like cell adhesion proteins are integral plasma membrane proteins. Their specific functions are unknown but they most likely play a critical role in the establishment and function of specific cell-cell neural connections. [provided by RefSeq, Jul 2008]

Canonical amino-acid sequenceUniProt

818 residues, UniProt reviewed canonical sequence.

>Q9Y5F3|PCDHB1
     1  MAGTRRKSLQ NRQVGSLLIF LCISVGDATT IRYSVAEEME SGSFVANVAK DLGLEVGKLA
    61  ARGARLVSEG NKMHFRLHRK TGDLFVKEKL DRESLCGKAD PCVLHFEVVL VEPLQSFRAE
   121  VRVFDINDNA PVFLNKEPLL KIPESTPLGS RFPLQSAQDL DVGLNGLQNY TLSANGYFHL
   181  HTRFCSHGPK YAELVLNKPL DREEQPEVNL TITAVDGGSP PKSGTAHIHV VVLDVNDHVP
   241  QFSRLVYRAQ VSENSPNGSL VATVTAVDLD EGTNKAITYS LAQNPEAILK TFQIDPQNGE
   301  VRLRGPLDFE AIETYDIDIQ ATDGGGLSAH SKVLVEVVDV NDNPPEVMVS SVSSPLPEDS
   361  PPQTVVALFT IRDRDIRVGG KVTCFLREDL PFVIKPTFGN SYSLVTDRSL DREEVSGYNI
   421  TIVAMDTGPP SLSAETMIEV LISDVNDNPP IFREDSYILT VRENNSPAVF IGKVHAEDLD
   481  LGENAQITYS LLPPKNGDLS VFAYISINSG NGKLYALRTM DYEAIQDFQF VVKATDGGFL
   541  SLSSQVTVRV VVLDDNDNRP MILYPLQNGT LPCNDLVPRS AEAGYLVTKV VAVDGDSGQN
   601  SWLSYHLLKA TDLGLFSVQR QNGEIHTLRQ ISERDPMMQK LIILVQDHGQ PALSTTVSLN
   661  ILLVDGFSEP YLQFQDPTKH SRKVNPSTKY LVISLVILSF LFLLSVIVIF IIHVYQKIKY
   721  REKFTIQEHF YDDCNFSNNL VQGQGNGSLS RPCPYEMCSA TGTGNSEFRF LKRFMPNFPF
   781  PHATGEIKME AGSSLPPNSD RNKSQRLEGH DQVSDDYM

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against PCDHB1 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): 0.38
Highest tissue expression: 1.3 nTPM

Expression across tissuesHPA

Tissue

skeletal muscle: 1.3 nTPM
pituitary gland: 0.5 nTPM
bone marrow: 0.4 nTPM
fallopian tube: 0.4 nTPM
pancreas: 0.4 nTPM
retina: 0.4 nTPM

Single-cell type

corticotrophs: 17 nCPM
ependymal cells: 5.3 nCPM
epididymal efferent duct ciliated cells: 3.8 nCPM
respiratory ciliated cells: 3.7 nCPM
thyrotrophs: 3.4 nCPM
pituicytes/fscs: 3.1 nCPM

Immune cell

basophil: 0.5 nTPM
neutrophil: 0.3 nTPM
naive B-cell: 0.2 nTPM
eosinophil: 0.1 nTPM
memory B-cell: 0.1 nTPM
NK-cell: 0.1 nTPM

Brain region

cerebellum: 3.9 nTPM
medulla oblongata: 3.1 nTPM
cerebral cortex: 3 nTPM
midbrain: 3 nTPM
pons: 3 nTPM
amygdala: 2.9 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): 1.31
gnomAD pLI: 0
gnomAD missense Z: 1.02
DepMap mean gene effect: -0.09
DepMap dependency class: selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 3% 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 PCDHB1 as an antibody target. Whether an autoantibody or antibody against PCDHB1 could matter depends on whether native PCDHB1 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

PCDHB1 is annotated at the cell surface, where native PCDHB1 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 PCDHB1 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

Loading the interactive Seroatlas protein explorer...