PDE1B

phosphodiesterase 1B, the group of Phosphodiesterases

Basic information

Region (hg38): 12:54549601-54579239

Previous symbols: [ "PDES1B" ]

Links

ENSG00000123360 ∙ NCBI:5153 ∙ OMIM:171891 ∙ HGNC:8775 ∙ Uniprot:Q01064 ∙ 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 PDE1B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDE1B 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	1
missense			27			27
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding						0
Total	0	0	28	0	1

Variants in PDE1B

This is a list of pathogenic ClinVar variants found in the PDE1B region.

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

Position	Type	Phenotype	Significance	ClinVar
12-54549925-C-A		not specified	Uncertain significance (Dec 02, 2024)
12-54549979-G-C		not specified	Uncertain significance (Dec 13, 2023)
12-54566979-G-A		not specified	Uncertain significance (Jun 26, 2024)
12-54567018-T-C		not specified	Uncertain significance (Jan 16, 2025)
12-54567080-G-A		not specified	Uncertain significance (Nov 14, 2023)
12-54567086-C-T		not specified	Uncertain significance (Dec 02, 2022)
12-54569212-C-T		Hypotonia;Cerebellar ataxia;Intellectual disability, moderate;Delayed speech and language development	Uncertain significance (Jun 20, 2023)
12-54569240-C-T		not specified	Uncertain significance (Sep 09, 2024)
12-54569248-C-T		not specified	Uncertain significance (Apr 25, 2023)
12-54569345-A-G		not specified	Uncertain significance (Jun 09, 2022)
12-54569358-C-T			Benign (Dec 31, 2019)
12-54569605-G-A		not specified	Uncertain significance (Apr 30, 2024)
12-54570258-C-G		not specified	Uncertain significance (Nov 29, 2023)
12-54570295-C-A		not specified	Uncertain significance (Feb 11, 2025)
12-54570337-A-G		not specified	Uncertain significance (Apr 08, 2022)
12-54572746-G-A		Hypotonia;Cerebellar ataxia;Intellectual disability, moderate;Delayed speech and language development	Uncertain significance (Jun 20, 2023)
12-54573239-T-C		not specified	Uncertain significance (Aug 10, 2021)
12-54573374-T-C		not specified	Uncertain significance (Dec 20, 2022)
12-54573423-G-A		not specified	Uncertain significance (Jul 25, 2024)
12-54573630-G-C		not specified	Uncertain significance (Oct 20, 2024)
12-54573663-T-A		not specified	Uncertain significance (Aug 21, 2024)
12-54575599-C-T		not specified	Uncertain significance (Jul 19, 2022)
12-54576038-C-G		not specified	Uncertain significance (Feb 07, 2025)
12-54576057-C-G		not specified	Uncertain significance (Jun 18, 2021)
12-54576061-C-T		not specified	Uncertain significance (Jan 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PDE1B	protein_coding	protein_coding	ENST00000243052	14	29890

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.336	0.664	125727	0	21	125748	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.27	203	317	0.641	0.0000181	3535
Missense in Polyphen		37	91.182	0.40578		961
Synonymous	1.39	102	122	0.839	0.00000677	1019
Loss of Function	3.95	7	30.6	0.229	0.00000166	334

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000304	0.000304
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000798	0.0000791
Middle Eastern	0.000109	0.000109
South Asian	0.0000980	0.0000980
Other	0.000163	0.000163

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. Has a preference for cGMP as a substrate. {ECO:0000269|PubMed:15260978}.
• Pathway: Calcium signaling pathway - Homo sapiens (human);Renin secretion - Homo sapiens (human);Purine metabolism - Homo sapiens (human);Taste transduction - Homo sapiens (human);Olfactory transduction - Homo sapiens (human);Morphine addiction - Homo sapiens (human);G Protein Signaling Pathways;Phosphodiesterases in neuronal function;Signaling by GPCR;Signal Transduction;G alpha (s) signalling events;Calmodulin induced events;CaM pathway;Cam-PDE 1 activation;Purine nucleotides nucleosides metabolism;Hemostasis;DAG and IP3 signaling;Ca-dependent events;PLC beta mediated events;G-protein mediated events;Opioid Signalling;G alpha (i) signalling events;cGMP effects;Nitric oxide stimulates guanylate cyclase;Platelet homeostasis;GPCR downstream signalling;Intracellular signaling by second messengers (Consensus)

Recessive Scores

• pRec: 0.157

Intolerance Scores

• loftool: 0.394
• rvis_EVS: -0.16
• rvis_percentile_EVS: 42.06

Haploinsufficiency Scores

• pHI: 0.384
• hipred: Y
• hipred_score: 0.775
• ghis: 0.573

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.100

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pde1b
• Phenotype: vision/eye phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: response to amphetamine;apoptotic process;G protein-coupled receptor signaling pathway;locomotory behavior;visual learning;monocyte differentiation;cellular response to macrophage colony-stimulating factor stimulus;regulation of dopamine metabolic process;serotonin metabolic process;cellular response to granulocyte macrophage colony-stimulating factor stimulus
• Cellular component: cytosol;neuronal cell body
• Molecular function: 3',5'-cyclic-AMP phosphodiesterase activity;calmodulin-dependent cyclic-nucleotide phosphodiesterase activity;protein binding;calmodulin binding;metal ion binding;3',5'-cyclic-GMP phosphodiesterase activity;calcium- and calmodulin-regulated 3',5'-cyclic-GMP phosphodiesterase activity