GeneBe

PDE6B

phosphodiesterase 6B, the group of Phosphodiesterases

Basic information

Region (hg38): 4:625573-670782

Previous symbols: [ "PDEB" ]

Links

ENSG00000133256 ∙ NCBI:5158 ∙ OMIM:180072 ∙ HGNC:8786 ∙ Uniprot:P35913 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • retinitis pigmentosa 40 (Definitive), mode of inheritance: AR
  • retinitis pigmentosa (Supportive), mode of inheritance: AD
  • congenital stationary night blindness (Supportive), mode of inheritance: AD
  • congenital stationary night blindness autosomal dominant 2 (Strong), mode of inheritance: AD
  • retinitis pigmentosa 40 (Strong), mode of inheritance: AR
  • congenital stationary night blindness autosomal dominant 2 (Strong), mode of inheritance: AD
  • retinitis pigmentosa 40 (Definitive), mode of inheritance: AR
  • congenital stationary night blindness autosomal dominant 2 (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Night blindness, congenital stationary, autosomal dominant 2; Joubert syndrome 22; Retinitis pigmentosa 40AD/ARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingMusculoskeletal; Neurologic; Ophthalmologic8394174; 8075643; 7599633; 17044014; 18854872; 20655036; 24166846; 30423442

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PDE6B gene.

  • not_provided (986 variants)
  • Retinal_dystrophy (150 variants)
  • Retinitis_pigmentosa (140 variants)
  • Inborn_genetic_diseases (112 variants)
  • Congenital_stationary_night_blindness_autosomal_dominant_2 (111 variants)
  • Retinitis_pigmentosa_40 (94 variants)
  • PDE6B-related_disorder (25 variants)
  • not_specified (20 variants)
  • Autosomal_recessive_retinitis_pigmentosa (6 variants)
  • Congenital_Stationary_Night_Blindness,_Dominant (3 variants)
  • Retinitis_Pigmentosa,_Recessive (2 variants)
  • High_myopia (1 variants)
  • Macular_dystrophy (1 variants)
  • Leber_congenital_amaurosis (1 variants)
  • Tyrosinase-positive_oculocutaneous_albinism (1 variants)
  • Cone-rod_dystrophy (1 variants)
  • See_cases (1 variants)
  • Rod-cone_dystrophy (1 variants)
  • Prostate_cancer (1 variants)
  • Congenital_stationary_night_blindness (1 variants)
  • Progressive_cone_dystrophy_(without_rod_involvement) (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDE6B gene is commonly pathogenic or not. These statistics are base on transcript: NM_000000283.4. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
17
clinvar
207
clinvar
3
clinvar
 227
missense
11
clinvar
42
clinvar
457
clinvar
43
clinvar
6
clinvar
 559
nonsense
29
clinvar
10
clinvar
 39
start loss
1
1
 2
frameshift
30
clinvar
18
clinvar
1
clinvar
1
clinvar
 50
splice donor/acceptor (+/-2bp)
17
clinvar
22
clinvar
2
clinvar
1
clinvar
 42
Total 87 93 478 252 9

Highest pathogenic variant AF is 0.00018555962

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
PDE6Bprotein_codingprotein_codingENST00000496514 2245199
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
2.62e-270.00075111701119785401257480.0354
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.7985725211.100.00003575664
Missense in Polyphen222204.811.08392289
Synonymous-1.422572301.120.00001861562
Loss of Function0.5064346.70.9200.00000235524

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.03210.0321
Ashkenazi Jewish0.01020.00997
East Asian0.0008160.000761
Finnish0.04330.0430
European (Non-Finnish)0.05760.0567
Middle Eastern0.0008160.000761
South Asian0.009280.00922
Other0.04020.0395

dbNSFP

Source: dbNSFP

Function
FUNCTION: This protein participates in processes of transmission and amplification of the visual signal. Necessary for the formation of a functional phosphodiesterase holoenzyme.;
Disease
DISEASE: Retinitis pigmentosa 40 (RP40) [MIM:613801]: A retinal dystrophy belonging to the group of pigmentary retinopathies. Retinitis pigmentosa is characterized by retinal pigment deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well. {ECO:0000269|PubMed:22334370, ECO:0000269|PubMed:8394174, ECO:0000269|PubMed:8557257, ECO:0000269|PubMed:8595886, ECO:0000269|PubMed:8698075, ECO:0000269|PubMed:8956055, ECO:0000269|PubMed:9543643}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Night blindness, congenital stationary, autosomal dominant 2 (CSNBAD2) [MIM:163500]: A non-progressive retinal disorder characterized by impaired night vision, often associated with nystagmus and myopia. {ECO:0000269|PubMed:8075643}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway
Purine metabolism - Homo sapiens (human);Phototransduction - Homo sapiens (human);Phosphodiesterases in neuronal function;Signaling by GPCR;Signaling by WNT;Signal Transduction;visual signal transduction;Purine nucleotides nucleosides metabolism;Ca2+ pathway;Beta-catenin independent WNT signaling;Visual signal transduction: Rods;G alpha (i) signalling events;Activation of the phototransduction cascade;Inactivation, recovery and regulation of the phototransduction cascade;The phototransduction cascade;Visual phototransduction;GPCR downstream signalling (Consensus)

Recessive Scores

pRec
0.556

Intolerance Scores

loftool
0.868
rvis_EVS
-0.54
rvis_percentile_EVS
20.05

Haploinsufficiency Scores

pHI
0.612
hipred
N
hipred_score
0.337
ghis
0.523

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.157

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Pde6b
Phenotype
nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); hearing/vestibular/ear phenotype; vision/eye phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); pigmentation phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype; cellular phenotype; craniofacial phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan);

Gene ontology

Biological process
G protein-coupled receptor signaling pathway;visual perception;phototransduction, visible light;rhodopsin mediated signaling pathway;regulation of rhodopsin mediated signaling pathway;regulation of cytosolic calcium ion concentration;retina development in camera-type eye
Cellular component
plasma membrane;photoreceptor disc membrane
Molecular function
metal ion binding;3',5'-cyclic-GMP phosphodiesterase activity