Seroatlas · Human Serome Atlas

PDE6D

Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta

Also known as: JBTS22, PDE6D_HUMAN

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

Protein identityUniProt · HPA

UniProt accession
O43924
Gene
PDE6D
Ensembl
ENSG00000156973
Chromosome
2
Canonical length
150 aa
Protein class
Disease related genes, Human disease related genes, Predicted intracellular proteins
Subcellular location
Vesicles

OverviewNCBI Gene

This gene encodes the delta subunit of rod-specific photoreceptor phosphodiesterase (PDE), a key enzyme in the phototransduction cascade. A similar protein in cow functions in solubilizing membrane-bound PDE. In addition to its role in the PDE complex, the encoded protein is thought to bind to prenyl groups of proteins to target them to subcellular organelles called cilia. Mutations in this gene are associated with Joubert syndrome-22. Alternative splicing results in multiple splice variants. [provided by RefSeq, Mar 2014]

Canonical amino-acid sequenceUniProt

150 residues, UniProt reviewed canonical sequence.

>O43924|PDE6D
     1  MSAKDERARE ILRGFKLNWM NLRDAETGKI LWQGTEDLSV PGVEHEARVP KKILKCKAVS
    61  RELNFSSTEQ MEKFRLEQKV YFKGQCLEEW FFEFGFVIPN STNTWQSLIE AAPESQMMPA
   121  SVLTGNVIIE TKFFDDDLLV STSRVRLFYV

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against PDE6D 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
Intracellular
Secreted
No
Transmembrane segments
0
Mean surface accessibility (rSASA)
0.28
Highest tissue expression
65 nTPM

Expression across tissuesHPA

Tissue

  • retina: 65 nTPM
  • spinal cord: 49 nTPM
  • midbrain: 44 nTPM
  • amygdala: 43 nTPM
  • basal ganglia: 42 nTPM
  • hippocampal formation: 41 nTPM

Single-cell type

  • late primary spermatocytes: 417 nCPM
  • early primary spermatocytes: 224 nCPM
  • late spermatids: 218 nCPM
  • early spermatids: 174 nCPM
  • cardiomyocytes: 137 nCPM
  • cone photoreceptor cells: 122 nCPM

Immune cell

  • basophil: 85 nTPM
  • T-reg: 85 nTPM
  • eosinophil: 69 nTPM
  • non-classical monocyte: 65 nTPM
  • plasmacytoid DC: 56 nTPM
  • naive B-cell: 56 nTPM

Brain region

  • white matter: 48 nTPM
  • cerebellum: 45 nTPM
  • basal ganglia: 44 nTPM
  • spinal cord: 43 nTPM
  • midbrain: 42 nTPM
  • thalamus: 42 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about PDE6D.

Disease | AllUniProt

Conditions PDE6D is implicated in, by any mechanism.

Disease | GeneticClinVar

8 pathogenic / likely-pathogenic of 75 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

  • Joubert syndrome 22

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)
1.02
gnomAD pLI
0.01
gnomAD missense Z
1.6
DepMap mean gene effect
0.04
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

InteractionsUniProt · HPA

Protein binding partners of PDE6D 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 PDE6D as an antibody target. Whether an autoantibody or antibody against PDE6D could matter depends on whether native PDE6D is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

PDE6D 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 PDE6D as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

Canonical record: https://seroatlas.com/gene/PDE6D. 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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