GeneBe

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.

  • not_specified (143 variants)
  • not_provided (11 variants)

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. These statistics are base on transcript: NM_000000922.4. 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
1
clinvar
5
clinvar
 6
missense
134
clinvar
10
clinvar
2
clinvar
 146
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 134 11 7
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
PDE3Bprotein_codingprotein_codingENST00000282096 16227082
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.00005721.0012555411931257480.000772
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.04825705730.9940.00002817171
Missense in Polyphen167210.510.793332634
Synonymous-1.512522231.130.00001082199
Loss of Function4.361750.40.3370.00000252598

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0005810.000580
Ashkenazi Jewish0.000.00
East Asian0.0001760.000163
Finnish0.001430.00143
European (Non-Finnish)0.001240.00122
Middle Eastern0.0001760.000163
South Asian0.00006550.0000653
Other0.0008150.000815

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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