Seroatlas · Human Serome Atlas

PDE6B

Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta

Also known as: CSNB3, CSNBAD2, PDE6B_HUMAN, PDEB, rd1, RP40

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

Protein identityUniProt · HPA

UniProt accession: P35913
Gene: PDE6B
Ensembl: ENSG00000133256
Chromosome: 4
Canonical length: 854 aa
Protein class: Disease related genes, Enzymes, Human disease related genes, Metabolic proteins, Predicted intracellular proteins
Subcellular location: Vesicles,Basal body,Cytosol

OverviewNCBI Gene

Photon absorption triggers a signaling cascade in rod photoreceptors that activates cGMP phosphodiesterase (PDE), resulting in the rapid hydrolysis of cGMP, closure of cGMP-gated cation channels, and hyperpolarization of the cell. PDE is a peripheral membrane heterotrimeric enzyme made up of alpha, beta, and gamma subunits. This gene encodes the beta subunit. Mutations in this gene result in retinitis pigmentosa and autosomal dominant congenital stationary night blindness. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2009]

Canonical amino-acid sequenceUniProt

854 residues, UniProt reviewed canonical sequence.

>P35913|PDE6B
     1  MSLSEEQARS FLDQNPDFAR QYFGKKLSPE NVAAACEDGC PPDCDSLRDL CQVEESTALL
    61  ELVQDMQESI NMERVVFKVL RRLCTLLQAD RCSLFMYRQR NGVAELATRL FSVQPDSVLE
   121  DCLVPPDSEI VFPLDIGVVG HVAQTKKMVN VEDVAECPHF SSFADELTDY KTKNMLATPI
   181  MNGKDVVAVI MAVNKLNGPF FTSEDEDVFL KYLNFATLYL KIYHLSYLHN CETRRGQVLL
   241  WSANKVFEEL TDIERQFHKA FYTVRAYLNC ERYSVGLLDM TKEKEFFDVW SVLMGESQPY
   301  SGPRTPDGRE IVFYKVIDYV LHGKEEIKVI PTPSADHWAL ASGLPSYVAE SGFICNIMNA
   361  SADEMFKFQE GALDDSGWLI KNVLSMPIVN KKEEIVGVAT FYNRKDGKPF DEQDEVLMES
   421  LTQFLGWSVM NTDTYDKMNK LENRKDIAQD MVLYHVKCDR DEIQLILPTR ARLGKEPADC
   481  DEDELGEILK EELPGPTTFD IYEFHFSDLE CTELDLVKCG IQMYYELGVV RKFQIPQEVL
   541  VRFLFSISKG YRRITYHNWR HGFNVAQTMF TLLMTGKLKS YYTDLEAFAM VTAGLCHDID
   601  HRGTNNLYQM KSQNPLAKLH GSSILERHHL EFGKFLLSEE TLNIYQNLNR RQHEHVIHLM
   661  DIAIIATDLA LYFKKRAMFQ KIVDESKNYQ DKKSWVEYLS LETTRKEIVM AMMMTACDLS
   721  AITKPWEVQS KVALLVAAEF WEQGDLERTV LDQQPIPMMD RNKAAELPKL QVGFIDFVCT
   781  FVYKEFSRFH EEILPMFDRL QNNRKEWKAL ADEYEAKVKA LEEKEEEERV AAKKVGTEIC
   841  NGGPAPKSST CCIL

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against PDE6B 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): 0.27
Highest tissue expression: 357 nTPM

Expression across tissuesHPA

Tissue

retina: 357 nTPM
spinal cord: 26 nTPM
hippocampal formation: 22 nTPM
midbrain: 21 nTPM
choroid plexus: 19 nTPM
basal ganglia: 18 nTPM

Single-cell type

rod photoreceptor cells: 628 nCPM
cone photoreceptor cells: 106 nCPM
oligodendrocytes: 68 nCPM
retinal bipolar cells: 49 nCPM
retinal pigment epithelial cells: 43 nCPM
retinal amacrine cells: 42 nCPM

Immune cell

naive B-cell: 22 nTPM
plasmacytoid DC: 18 nTPM
basophil: 17 nTPM
naive CD8 T-cell: 16 nTPM
T-reg: 16 nTPM
naive CD4 T-cell: 15 nTPM

Brain region

white matter: 99 nTPM
pons: 75 nTPM
basal ganglia: 74 nTPM
cerebral cortex: 74 nTPM
thalamus: 72 nTPM
medulla oblongata: 71 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about PDE6B.

Disease | AllUniProt

Conditions PDE6B is implicated in, by any mechanism.

Retinitis pigmentosa 40 (RP40) MIM:613801
Night blindness, congenital stationary, autosomal dominant 2 (CSNBAD2) MIM:163500

Disease | GeneticClinVar

173 pathogenic / likely-pathogenic of 1,291 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

Retinitis pigmentosa 40
Retinal dystrophy
Retinitis pigmentosa
Congenital stationary night blindness autosomal dominant 2
PDE6B-related disorder

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): 1.19
gnomAD pLI: 0
gnomAD missense Z: -0.8
DepMap mean gene effect: 0.03
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 PDE6B as an antibody target. Whether an autoantibody or antibody against PDE6B could matter depends on whether native PDE6B is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

PDE6B 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 PDE6B as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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