PDE3B

phosphodiesterase 3B, the group of Phosphodiesterases

Basic information

Region (hg38): 11:14643804-14872044

Links

ENSG00000152270 ∙ NCBI:5140 ∙ OMIM:602047 ∙ HGNC:8779 ∙ Uniprot:Q13370 ∙ 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 PDE3B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDE3B 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	5	6
missense			55	6	2	63
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					2	2
Total	0	0	55	7	9

Variants in PDE3B

This is a list of pathogenic ClinVar variants found in the PDE3B region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
11-14644110-G-T		not specified	Uncertain significance (Jun 07, 2023)
11-14644127-G-A		not specified	Uncertain significance (May 09, 2022)
11-14644142-C-A		not specified	Uncertain significance (May 03, 2023)
11-14644142-C-T		not specified	Uncertain significance (Mar 18, 2024)
11-14644149-A-G		not specified	Uncertain significance (Jan 04, 2022)
11-14644152-G-A		not specified	Uncertain significance (Dec 20, 2023)
11-14644163-G-C		not specified	Uncertain significance (Aug 28, 2023)
11-14644186-C-A		not specified	Uncertain significance (Nov 09, 2024)
11-14644197-A-C		not specified	Uncertain significance (Oct 03, 2024)
11-14644208-C-T		not specified	Uncertain significance (Dec 17, 2023)
11-14644215-T-G		not specified	Uncertain significance (Jan 22, 2024)
11-14644226-C-T		not specified	Uncertain significance (Apr 01, 2024)
11-14644244-G-A		not specified	Uncertain significance (Sep 26, 2024)
11-14644304-C-G		not specified	Uncertain significance (Aug 23, 2021)
11-14644305-G-C		not specified	Uncertain significance (Dec 08, 2023)
11-14644305-G-T		not specified	Uncertain significance (Mar 20, 2024)
11-14644326-C-T		not specified	Uncertain significance (Sep 29, 2023)
11-14644347-C-T		not specified	Uncertain significance (Nov 17, 2023)
11-14644386-G-A		not specified	Uncertain significance (May 02, 2024)
11-14644432-G-C		not specified	Uncertain significance (Jul 08, 2022)
11-14644436-C-T		not specified	Uncertain significance (Dec 02, 2022)
11-14644467-T-G		not specified	Uncertain significance (Dec 07, 2021)
11-14644484-A-G		not specified	Uncertain significance (Apr 26, 2023)
11-14644527-C-G		not specified	Uncertain significance (Oct 14, 2023)
11-14644551-C-T		not specified	Uncertain significance (May 22, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PDE3B	protein_coding	protein_coding	ENST00000282096	16	227082

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000572	1.00	125554	1	193	125748	0.000772

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0482	570	573	0.994	0.0000281	7171
Missense in Polyphen		167	210.51	0.79333		2634
Synonymous	-1.51	252	223	1.13	0.0000108	2199
Loss of Function	4.36	17	50.4	0.337	0.00000252	598

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000581	0.000580
Ashkenazi Jewish	0.00	0.00
East Asian	0.000176	0.000163
Finnish	0.00143	0.00143
European (Non-Finnish)	0.00124	0.00122
Middle Eastern	0.000176	0.000163
South Asian	0.0000655	0.0000653
Other	0.000815	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cyclic nucleotide phosphodiesterase with a dual- specificity for the second messengers cAMP and cGMP, which are key regulators of many important physiological processes. May play a role in fat metabolism. Regulates cAMP binding of RAPGEF3. Through simultaneous binding to RAPGEF3 and PIK3R6 assembles a signaling complex in which the PI3K gamma complex is activated by RAPGEF3 and which is involved in angiogenesis. {ECO:0000269|PubMed:15147193, ECO:0000269|PubMed:21393242}.
• Pathway: PKB-mediated events;Regulation of lipolysis in adipocytes - Homo sapiens (human);Glucagon signaling pathway - Homo sapiens (human);cAMP signaling pathway - Homo sapiens (human);Apelin signaling pathway - Homo sapiens (human);Renin secretion - Homo sapiens (human);Purine metabolism - Homo sapiens (human);cGMP-PKG signaling pathway - Homo sapiens (human);Morphine addiction - Homo sapiens (human);Insulin signaling pathway - Homo sapiens (human);Progesterone-mediated oocyte maturation - Homo sapiens (human);Leptin signaling pathway;JAK-STAT;Phosphodiesterases in neuronal function;Signaling by GPCR;Signal Transduction;PDE3B signalling;PI3K Cascade;IRS-mediated signalling;Insulin receptor signalling cascade;Signaling by Insulin receptor;G alpha (s) signalling events;actions of nitric oxide in the heart;Purine nucleotides nucleosides metabolism;Hemostasis;Class IB PI3K non-lipid kinase events;IRS-related events triggered by IGF1R;IGF1R signaling cascade;Signaling by Receptor Tyrosine Kinases;cGMP effects;Nitric oxide stimulates guanylate cyclase;Platelet homeostasis;GPCR downstream signalling;Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) (Consensus)

Recessive Scores

• pRec: 0.398

Intolerance Scores

• loftool: 0.497
• rvis_EVS: 0.07
• rvis_percentile_EVS: 59.16

Haploinsufficiency Scores

• pHI: 0.186
• hipred: Y
• hipred_score: 0.694
• ghis: 0.439

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.557

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Pde3b
• 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); adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; pigmentation phenotype

Gene ontology

• Biological process: angiogenesis;negative regulation of cell adhesion;G protein-coupled receptor signaling pathway;negative regulation of angiogenesis;cellular response to insulin stimulus;negative regulation of cell adhesion mediated by integrin;negative regulation of cAMP-mediated signaling;negative regulation of lipid catabolic process
• Cellular component: endoplasmic reticulum;Golgi apparatus;cytosol;membrane;integral component of membrane;guanyl-nucleotide exchange factor complex
• Molecular function: 3',5'-cyclic-nucleotide phosphodiesterase activity;3',5'-cyclic-AMP phosphodiesterase activity;cGMP-inhibited cyclic-nucleotide phosphodiesterase activity;protein binding;protein kinase B binding;metal ion binding;3',5'-cyclic-GMP phosphodiesterase activity