Seroatlas · Human Serome Atlas

PCDHB16

Protocadherin beta-16

Also known as: KIAA1621, ME1, PCDBG_HUMAN, PCDH-BETA16, PCDH3X, PCDHB8a

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

Protein identityUniProt · HPA

UniProt accession: Q9NRJ7
Gene: PCDHB16
Ensembl: ENSG00000272674
Chromosome: 5
Canonical length: 776 aa
Protein class: Predicted intracellular proteins, Predicted membrane proteins
Subcellular location: Vesicles,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

776 residues, UniProt reviewed canonical sequence.

>Q9NRJ7|PCDHB16
     1  MEIGWMHNRR QRQVLVFFVL LSLSGAGAEL GSYSVVEETE RGSFVANLGK DLGLGLTEMS
    61  TRKARIISQG NKQHLQLKAQ TGDLLINEKL DREELCGPTE PCILHFQVLM ENPLEIFQAE
   121  LRVIDINDHS PMFTEKEMIL KIPENSPLGT EFPLNHALDL DVGSNNVQNY KISPSSHFRV
   181  LIHEFRDGRK YPELVLDKEL DREEEPQLRL TLTALDGGSP PRSGTAQVRI EVVDINDNAP
   241  EFEQPIYKVQ IPENSPLGSL VATVSARDLD GGANGKISYT LFQPSEDISK TLEVNPMTGE
   301  VRLRKQVDFE MVTSYEVRIK ATDGGGLSGK CTLLLQVVDV NDNPPQVTMS ALTSPIPENS
   361  PEIVVAVFSV SDPDSGNNGK TISSIQEDLP FLLKPSVKNF YTLVTERALD REARAEYNIT
   421  LTVTDMGTPR LKTEHNITVQ ISDVNDNAPT FTQTSYTLFV RENNSPALHI GSVSATDRDS
   481  GTNAQVTYSL LPPQDPHLPL ASLVSINADN GHLFALRSLD YEALQAFEFR VGATDRGSPA
   541  LSREALVRVL VLDANDNSPF VLYPLQNGSA PCTELVPRAA EPGYLVTKVV AVDGDSGQNA
   601  WLSYQLLKAT EPGLFGVWAH NGEVRTARLL SERDAAKQRL VVLVKDNGEP PRSATATLHV
   661  LLVDGFSQPF LPLPEAAPGQ TQANSLTVYL VVALASVSSL FLFSVLLFVA VRLCRRSRAA
   721  SVGRCSMPEG PFPGRLVDVS GTGTLSQSYQ YEVCLTGGSE TSEFKFLKPI IPNFSP

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against PCDHB16 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): 0.36
Highest tissue expression: 5.3 nTPM

Expression across tissuesHPA

Tissue

blood vessel: 5.3 nTPM
ovary: 4.9 nTPM
epididymis: 4.5 nTPM
endometrium: 4.3 nTPM
parathyroid gland: 4.1 nTPM
tongue: 3.1 nTPM

Single-cell type

podocytes: 1.3 nCPM
endometrial stromal cells: 0.6 nCPM
schwann cells: 0.6 nCPM
lactotrophs: 0.5 nCPM
bergmann glia: 0.4 nCPM
corticotrophs: 0.3 nCPM

Immune cell

neutrophil: 0.1 nTPM
basophil: 0 nTPM
classical monocyte: 0 nTPM
eosinophil: 0 nTPM
gdT-cell: 0 nTPM
intermediate monocyte: 0 nTPM

Brain region

cerebellum: 9.6 nTPM
medulla oblongata: 9.6 nTPM
white matter: 9.6 nTPM
cerebral cortex: 8.9 nTPM
hippocampal formation: 8.6 nTPM
spinal cord: 8.5 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): 1.25
gnomAD pLI: 0
gnomAD missense Z: -1.01
DepMap mean gene effect: -0.04
DepMap dependency class: selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 5% 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 PCDHB16 as an antibody target. Whether an autoantibody or antibody against PCDHB16 could matter depends on whether native PCDHB16 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

PCDHB16 is annotated at the cell surface, where native PCDHB16 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 PCDHB16 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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