PDE4B
phosphodiesterase 4B, the group of Phosphodiesterases
Basic information
Region (hg38): 1:65792514-66374579
Previous symbols: [ "DPDE4" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDE4B 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 | 4 | |||||
| missense | 13 | 14 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 13 | 1 | 4 |
Variants in PDE4B
This is a list of pathogenic ClinVar variants found in the PDE4B region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-66247566-C-T | not specified | Uncertain significance (Jan 30, 2024) | ||
| 1-66247621-C-T | not specified | Uncertain significance (Apr 09, 2024) | ||
| 1-66247627-C-T | not specified | Uncertain significance (Sep 21, 2021) | ||
| 1-66332511-A-G | not specified | Uncertain significance (Jul 12, 2023) | ||
| 1-66332547-A-G | not specified | Uncertain significance (Dec 21, 2023) | ||
| 1-66363203-C-T | Likely benign (Dec 17, 2018) | |||
| 1-66365723-C-T | Benign (Dec 31, 2019) | |||
| 1-66367799-G-A | not specified | Uncertain significance (Sep 26, 2022) | ||
| 1-66367818-C-T | not specified | Uncertain significance (May 17, 2023) | ||
| 1-66368007-C-T | not specified | Uncertain significance (Oct 03, 2022) | ||
| 1-66368058-G-A | not specified | Uncertain significance (Apr 12, 2024) | ||
| 1-66368912-G-A | Benign (Dec 31, 2019) | |||
| 1-66372393-C-T | Benign (Dec 31, 2019) | |||
| 1-66372428-G-A | not specified | Uncertain significance (Nov 17, 2022) | ||
| 1-66372511-C-G | not specified | Uncertain significance (Jun 09, 2022) | ||
| 1-66372533-C-T | not specified | Uncertain significance (May 10, 2022) | ||
| 1-66372574-A-T | Benign (Dec 31, 2019) | |||
| 1-66372587-C-T | not specified | Uncertain significance (Aug 26, 2022) | ||
| 1-66372630-G-C | not specified | Uncertain significance (Jul 19, 2022) | ||
| 1-66372667-G-A | not specified | Uncertain significance (Mar 01, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PDE4B | protein_coding | protein_coding | ENST00000329654 | 16 | 582063 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.475 | 0.525 | 125733 | 0 | 15 | 125748 | 0.0000596 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.77 | 249 | 406 | 0.613 | 0.0000210 | 4916 |
| Missense in Polyphen | 76 | 170.54 | 0.44565 | 2095 | ||
| Synonymous | 0.654 | 141 | 151 | 0.932 | 0.00000841 | 1363 |
| Loss of Function | 4.38 | 8 | 36.6 | 0.219 | 0.00000181 | 448 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000179 | 0.000179 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000109 | 0.000109 |
| Finnish | 0.0000934 | 0.0000924 |
| European (Non-Finnish) | 0.0000528 | 0.0000527 |
| Middle Eastern | 0.000109 | 0.000109 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Hydrolyzes the second messenger cAMP, which is a key regulator of many important physiological processes. May be involved in mediating central nervous system effects of therapeutic agents ranging from antidepressants to antiasthmatic and anti-inflammatory agents. {ECO:0000269|PubMed:10846163, ECO:0000269|PubMed:15003452}.;
- Pathway
- cAMP signaling pathway - Homo sapiens (human);Purine metabolism - Homo sapiens (human);Morphine addiction - Homo sapiens (human);Beta-agonist/Beta-blocker Pathway, Pharmacodynamics;Glucocorticoid Receptor Pathway;Nuclear Receptors Meta-Pathway;Myometrial Relaxation and Contraction Pathways;G Protein Signaling Pathways;Phosphodiesterases in neuronal function;Signaling by GPCR;Signal Transduction;G alpha (s) signalling events;DARPP-32 events;Purine nucleotides nucleosides metabolism;Opioid Signalling;G alpha (i) signalling events;GPCR downstream signalling
(Consensus)
Recessive Scores
- pRec
- 0.407
Intolerance Scores
- loftool
- 0.404
- rvis_EVS
- -0.69
- rvis_percentile_EVS
- 15.27
Haploinsufficiency Scores
- pHI
- 0.847
- hipred
- Y
- hipred_score
- 0.715
- ghis
- 0.434
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.644
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Pde4b
- Phenotype
- cellular phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); 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); immune system phenotype;
Gene ontology
- Biological process
- neutrophil homeostasis;cAMP catabolic process;G protein-coupled receptor signaling pathway;neutrophil chemotaxis;positive regulation of interferon-gamma production;positive regulation of interleukin-2 production;cellular response to drug;T cell receptor signaling pathway;leukocyte migration;cellular response to lipopolysaccharide;cellular response to epinephrine stimulus;regulation of cardiac muscle cell contraction;regulation of high voltage-gated calcium channel activity;negative regulation of relaxation of cardiac muscle
- Cellular component
- gamma-tubulin complex;centrosome;cytosol;voltage-gated calcium channel complex;synaptic vesicle;postsynaptic density;Z disc;dendritic spine;excitatory synapse
- Molecular function
- 3',5'-cyclic-AMP phosphodiesterase activity;protein binding;cAMP binding;gamma-tubulin binding;ion channel binding;metal ion binding