PDE6B
Basic information
Region (hg38): 4:625573-670782
Previous symbols: [ "PDEB" ]
Links
Phenotypes
GenCC
Source:
- 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
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Night blindness, congenital stationary, autosomal dominant 2; Joubert syndrome 22; Retinitis pigmentosa 40 | AD/AR | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Musculoskeletal; Neurologic; Ophthalmologic | 8394174; 8075643; 7599633; 17044014; 18854872; 20655036; 24166846; 30423442 |
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (52 variants)
- Retinitis pigmentosa (17 variants)
- Retinitis pigmentosa 40 (16 variants)
- Retinal dystrophy (12 variants)
- Retinitis pigmentosa 40;Congenital stationary night blindness autosomal dominant 2 (2 variants)
- Autosomal recessive retinitis pigmentosa (1 variants)
- Congenital stationary night blindness autosomal dominant 2;Retinitis pigmentosa 40 (1 variants)
- Tyrosinase-positive oculocutaneous albinism (1 variants)
- PDE6B-related disorder (1 variants)
- Congenital stationary night blindness autosomal dominant 2 (1 variants)
- Cone-rod dystrophy (1 variants)
- See cases (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.
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.
Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
---|---|---|---|---|---|---|
synonymous | 15 | 169 | 187 | |||
missense | 17 | 399 | 434 | |||
nonsense | 25 | 30 | ||||
start loss | 1 | |||||
frameshift | 20 | 11 | 31 | |||
inframe indel | 16 | 17 | ||||
splice donor/acceptor (+/-2bp) | 11 | 20 | 33 | |||
splice region | 1 | 24 | 35 | 2 | 62 | |
non coding | 24 | 103 | 42 | 171 | ||
Total | 64 | 54 | 457 | 279 | 50 |
Highest pathogenic variant AF is 0.000184
Variants in PDE6B
This is a list of pathogenic ClinVar variants found in the PDE6B region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
4-625627-A-G | Retinitis pigmentosa | Likely pathogenic (Jan 01, 2015) | ||
4-625629-G-T | Uncertain significance (Oct 04, 2019) | |||
4-625635-C-T | Likely benign (Dec 30, 2021) | |||
4-625648-GC-G | Pathogenic (Aug 10, 2023) | |||
4-625649-C-T | Uncertain significance (Dec 14, 2023) | |||
4-625651-C-T | Inborn genetic diseases | Conflicting classifications of pathogenicity (Jan 04, 2024) | ||
4-625652-G-A | Benign (Jan 31, 2024) | |||
4-625656-C-T | Likely benign (Apr 20, 2023) | |||
4-625672-C-G | Uncertain significance (Jan 15, 2022) | |||
4-625674-C-T | PDE6B-related disorder | Likely benign (Dec 11, 2023) | ||
4-625675-G-A | Uncertain significance (Aug 09, 2022) | |||
4-625675-G-T | Uncertain significance (Nov 13, 2023) | |||
4-625681-G-T | Inborn genetic diseases | Uncertain significance (Aug 16, 2022) | ||
4-625684-C-T | Uncertain significance (Sep 06, 2023) | |||
4-625685-G-A | Retinitis pigmentosa • Congenital stationary night blindness autosomal dominant 2 • Inborn genetic diseases | Conflicting classifications of pathogenicity (Sep 26, 2023) | ||
4-625697-G-C | Uncertain significance (Jan 12, 2022) | |||
4-625700-A-G | Inborn genetic diseases | Uncertain significance (Jun 27, 2023) | ||
4-625704-A-G | Likely benign (Sep 02, 2020) | |||
4-625705-CTG-C | Pathogenic (Jul 12, 2022) | |||
4-625712-C-G | Uncertain significance (Aug 07, 2023) | |||
4-625713-T-G | Likely benign (Jul 19, 2022) | |||
4-625719-T-A | Uncertain significance (Nov 27, 2021) | |||
4-625721-T-A | Uncertain significance (Dec 05, 2022) | |||
4-625726-G-A | Uncertain significance (May 08, 2023) | |||
4-625726-G-C | Uncertain significance (Sep 01, 2021) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
PDE6B | protein_coding | protein_coding | ENST00000496514 | 22 | 45199 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
2.62e-27 | 0.000751 | 117011 | 197 | 8540 | 125748 | 0.0354 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -0.798 | 572 | 521 | 1.10 | 0.0000357 | 5664 |
Missense in Polyphen | 222 | 204.81 | 1.0839 | 2289 | ||
Synonymous | -1.42 | 257 | 230 | 1.12 | 0.0000186 | 1562 |
Loss of Function | 0.506 | 43 | 46.7 | 0.920 | 0.00000235 | 524 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0321 | 0.0321 |
Ashkenazi Jewish | 0.0102 | 0.00997 |
East Asian | 0.000816 | 0.000761 |
Finnish | 0.0433 | 0.0430 |
European (Non-Finnish) | 0.0576 | 0.0567 |
Middle Eastern | 0.000816 | 0.000761 |
South Asian | 0.00928 | 0.00922 |
Other | 0.0402 | 0.0395 |
dbNSFP
Source:
- 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
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
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