AtlasGene
PDE6B
phosphodiesterase 6B
- HGNC 8786↗(opens in a new tab)
- Ensembl gene ENSG00000133256↗(opens in a new tab)
- NCBI Gene 5158↗(opens in a new tab)
Summary
- Cytogenetic location
- 4p16.3
- Coordinates
- Chromosome 4: 625,573–670,782 (GRCh38)
- Exons
- 22 exons across 45.2 kb
- Protein
- 854 amino acids
- Also known as
- CSNB3, rd1, RP40, CSNBAD2
- Previous symbols
- PDEB
- MANE Select transcript
- ENST00000496514.6NM_000283.4
- Locus type
- Protein-coding
- Very high
- Confident
- Low
- Very low
AtlasThis page as data
Add .json to the page's address, or ask for application/json, to read it as JSON.
library(jsonlite)
url <- "https://dantelabs.com/genes/pde6b.json"
page <- fromJSON(url)
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Get my Genome TestCurated reports relevant to this gene
Congenital Stationary Night Blindness
A group of mostly non-progressive retinal conditions, including Oguchi disease, caused by changes in genes such as NYX, CACNA1F, TRPM1, GRM6, GPR179 and SAG, often with nystagmus or short-sightedness.
- 3 GenCC submitters rate it definitive or strong
▶Actionability
A genetic diagnosis explains the symptoms, helps distinguish the condition from progressive retinal diseases and informs family counselling.
Broader groupings
Retinitis Pigmentosa
One of 77 genes linked to it
A group of inherited retinal dystrophies with progressive loss of rod and then cone photoreceptors, causing night blindness and gradual loss of peripheral vision.
- 4 GenCC submitters rate it definitive or strong
How PDE6B is laid out
- Coding sequence
- Untranslated region
- Intron
- Direction of transcription
- Known disease-causing sites
- Stretches short reads find hard
Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.
Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).
Nearby genes from Ensembl release 116, on GRCh38.
Exons make up 3.3 kb of the gene's 45.2 kb; 2,565 of those bases code for the protein.
Sequencing PDE6B
4Low
How hard PDE6B is to sequence with short reads, out of 100Each bar is the share of PDE6B's exon bases in that kind of difficult region. The score weighs them by how much each costs a short-read call: 0 when no base is in any, 100 when every base is in all of them.
- MappabilityStretches where 100 or 250 bp reads cannot be placed uniquely, so a call there may be missing or wrong. Weight 35%.0%
- HomologySegmental duplications: copies elsewhere in the genome, such as paralogues and pseudogenes, at 90% identity or more. Weight 30%.0%
- RepeatsTandem repeats and runs of one base, which reads slip on and may not span. Weight 15%.2.2%
- GC contentWindows under 25% or over 65% G and C, which library preparation covers thinly. Weight 10%.33%
- Reference coverageGaps in the reference assembly nearby, where there is no sequence for reads to align to. Weight 10%.0%
84
positions in PDE6B where ClinVar classes a change as pathogenic or likely pathogenic
None of them falls in a region short reads find hard.
A whole genome covers all 45.2 kb of PDE6B, introns included, not only the 3.3 kb of exons.
Genes linked to the same conditions
- RHOrhodopsinShares 2 conditions
- SAGS-antigen visual arrestinShares 2 conditions
- ABCA4ATP binding cassette subfamily A member 4Shares 1 condition
- AGBL5AGBL carboxypeptidase 5Shares 1 condition
- AHRaryl hydrocarbon receptorShares 1 condition
- ARHGEF18Rho/Rac guanine nucleotide exchange factor 18Shares 1 condition
- ARL2BPARF like GTPase 2 binding proteinShares 1 condition
- ARL3ARF like GTPase 3Shares 1 condition
- ARL6ARF like GTPase 6Shares 1 condition
- BBS2Bardet-Biedl syndrome 2Shares 1 condition
- BEST1bestrophin 1Shares 1 condition
- CA4carbonic anhydrase 4Shares 1 condition
Traits linked to PDE6B
The Human Phenotype Ontology lists these as features of the rare conditions PDE6B can cause. Each trait's page lists the other genes linked to it.
Abnormality of the eye
- Abnormal light- and dark-adapted electroretinogram
- Clouding of the lens of the eye
- Difficulties with night vision
- Moderate myopia
- Night blindness since birth
- Spicular pigmentation of the retina
- Abnormal electroretinogram
- Abnormal retinal pigmentation
Show 23 more traits
- Blindness
- Extreme sensitivity of the eyes to light
- Involuntary, rapid, rhythmic eye movements
- Optic atrophy
- Progressive night blindness
- Retina degeneration
- Visual impairment
- Abnormal central response of multifocal electroretinogram
- Abnormal full-field electroretinogram
- Bulging cornea
- Cystoid macular edema
- Eye muscle paralysis
- Glaucoma
- Loss of peripheral vision
- Optic disc drusen
- Optic disc pallor
- Photoreceptor outer segment loss on macular OCT
- Posterior subcapsular cataract
- Retinal atrophy
- Abnormal color vision
- Decreased clarity of vision
- Photopsia
- Rod-cone dystrophy
External links
Gene records
Transcript
Protein
Where this comes from
- HGNC: the gene's symbol, name, other symbols and location.
- MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
- GenCC and ClinGen, released 2026-10-17: which conditions the gene is linked to, and how strongly.
- The ACMG secondary findings list, SF v3.2.
- ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
- The Genome in a Bottle genome stratifications, from NIST: the sequencing difficulty score.
- The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
- Data release 2026.10.18-e609d43e.
Cite this page
Dante Labs. (n.d.). PDE6B gene: phosphodiesterase 6B. Retrieved 18 October 2026, from https://dantelabs.com/genes/pde6b
Dante Labs. PDE6B gene: phosphodiesterase 6B [Internet]. [cited 18 October 2026]. Available from: https://dantelabs.com/genes/pde6b
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