GeneBe

PDE3B

protein-coding

phosphodiesterase 3B, the group of Phosphodiesterases

Gene summary

Enables 3',5'-cyclic-AMP phosphodiesterase activity. Involved in several processes, including negative regulation of angiogenesis; negative regulation of lipid catabolic process; and regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction. Located in membrane. Part of guanyl-nucleotide exchange factor complex. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_000922.4

Inheritance

—

ClinVar variants

U:163B:18

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.34

Max pathogenic AF

—

Genomic locus

chr11:14,643,804-14,872,044

External References & Databases

Ensembl (ENSG00000152270)NCBI Gene (5140)OMIM (602047)HGNC:8779GenCCUniProt (Q13370)AlphaFoldClinVar (PDE3B)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~228.2 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PDE3B variants in ClinVar

2 Conditions Cataloged
not specifiedTotal: 162
not providedTotal: 11

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_000922.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
2
clinvar
1
clinvar
5
clinvar
 8
missense
157
clinvar
10
clinvar
2
clinvar
 169
nonsense
1
clinvar
 1
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
3
clinvar
 3
Total00163117181
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 45 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_000922.4RefSeqNP_000913.216MANE Select
ENST00000282096.9EnsemblENSP00000282096.416MANE Select
NM_001363569.2RefSeqNP_001350498.116Standard
NM_001363570.2RefSeqNP_001350499.117Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • 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)

Biological Process

  • angiogenesis
  • negative regulation of cell adhesion
  • G protein-coupled receptor signaling pathway
  • negative regulation of angiogenesis
  • cellular response to insulin stimulus

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

Cellular Component

  • endoplasmic reticulum
  • Golgi apparatus
  • cytosol
  • membrane
  • integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000282096
Coding exons
16
Length
227082
Individuals with no LoFs
125554
Homozygous LoFs
1
Heterozygous LoFs
193
Defined
125748
p
0.000772
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.04825705730.9940.00002817171
Missense (PolyPhen)167210.510.793332634
Synonymous-1.512522231.130.00001082199
Loss of Function4.361750.40.3370.00000252598

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000310.00031rare
Latino/Admixed American0.000270.00026rare
Ashkenazi Jewish00.0absent
East Asian0.000180.00016rare
Finnish0.00140.0014notable
European (Non-Finnish)0.00120.0012notable
South Asian0.0000660.000065rare
Other0.000820.00081rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec
0.398

Intolerance Scores

LoFtool
0.497
RVIS EVS
0.07
RVIS percentile EVS
59.16

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.557

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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