Seroatlas · Human Serome Atlas

PDCD6

Programmed cell death protein 6

Also known as: ALG-2, PDCD6_HUMAN, PEF1B

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

Protein identityUniProt · HPA

UniProt accession
O75340
Gene
PDCD6
Ensembl
ENSG00000249915
Chromosome
5
Canonical length
191 aa
Protein class
Plasma proteins, Predicted intracellular proteins, Transporters
Subcellular location
Nucleoplasm,Cytosol
Quaternary structure
Homodimer

OverviewNCBI Gene

This gene encodes a calcium-binding protein belonging to the penta-EF-hand protein family. Calcium binding is important for homodimerization and for conformational changes required for binding to other protein partners. This gene product participates in T cell receptor-, Fas-, and glucocorticoid-induced programmed cell death. In mice deficient for this gene product, however, apoptosis was not blocked suggesting this gene product is functionally redundant. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene, and a pseudogene of this gene is also located on the short arm of chromosome 5. [provided by RefSeq, May 2012]

Canonical amino-acid sequenceUniProt

191 residues, UniProt reviewed canonical sequence.

>O75340|PDCD6
     1  MAAYSYRPGP GAGPGPAAGA ALPDQSFLWN VFQRVDKDRS GVISDTELQQ ALSNGTWTPF
    61  NPVTVRSIIS MFDRENKAGV NFSEFTGVWK YITDWQNVFR TYDRDNSGMI DKNELKQALS
   121  GFGYRLSDQF HDILIRKFDR QGRGQIAFDD FIQGCIVLQR LTDIFRRYDT DQDGWIQVSY
   181  EQYLSMVFSI V

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against PDCD6 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
Other membrane
Secreted
No
Transmembrane segments
0
Mean surface accessibility (rSASA)
0.31
Highest tissue expression
132 nTPM

Expression across tissuesHPA

Tissue

  • esophagus: 132 nTPM
  • adrenal gland: 105 nTPM
  • epididymis: 103 nTPM
  • kidney: 99 nTPM
  • choroid plexus: 98 nTPM
  • cerebral cortex: 97 nTPM

Single-cell type

  • oligodendrocytes: 61 nCPM
  • other brain neurons: 58 nCPM
  • choroid plexus epithelial cells: 57 nCPM
  • brain excitatory neurons: 57 nCPM
  • podocytes: 56 nCPM
  • microglia: 53 nCPM

Immune cell

  • total PBMC: 356 nTPM
  • eosinophil: 286 nTPM
  • NK-cell: 262 nTPM
  • memory B-cell: 254 nTPM
  • T-reg: 237 nTPM
  • neutrophil: 233 nTPM

Brain region

  • white matter: 77 nTPM
  • cerebellum: 68 nTPM
  • spinal cord: 65 nTPM
  • hypothalamus: 64 nTPM
  • medulla oblongata: 63 nTPM
  • pons: 60 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)
0.95
gnomAD pLI
0.01
gnomAD missense Z
0.45
DepMap mean gene effect
-0.15
DepMap dependency class
selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 12% 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

InteractionsUniProt · HPA

Protein binding partners of PDCD6 in the human serome: UniProt-annotated complex subunits plus reported interactors. Each links to its own Seroatlas record.

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads PDCD6 as an antibody target. Whether an autoantibody or antibody against PDCD6 could matter depends on whether native PDCD6 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

PDCD6 is annotated as predominantly intracellular. Intracellular proteins are common autoantibody markers, becoming visible to the immune system after cell injury or altered processing, but are usually markers of disease rather than direct drivers.

Annotation status

The present source text does not explicitly label PDCD6 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

Canonical record: https://seroatlas.com/gene/PDCD6. 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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