PDE4B

phosphodiesterase 4B, the group of Phosphodiesterases

Basic information

Region (hg38): 1:65792513-66374579

Previous symbols: [ "DPDE4" ]

Links

ENSG00000184588 ∙ NCBI:5142 ∙ OMIM:600127 ∙ HGNC:8781 ∙ Uniprot:Q07343 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PDE4B gene.

• Inborn genetic diseases (10 variants)
• not provided (5 variants)

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				1	3	4
missense			10		1	11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	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)
1-66247627-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)
1-66368912-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: gnomAD

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: dbNSFP

• 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