PDE7B

phosphodiesterase 7B, the group of Phosphodiesterases

Basic information

Region (hg38): 6:135851700-136195574

Links

ENSG00000171408 ∙ NCBI:27115 ∙ OMIM:604645 ∙ HGNC:8792 ∙ Uniprot:Q9NP56 ∙ 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 PDE7B 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 PDE7B 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					3	3
missense			10		2	12
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	0	5

Variants in PDE7B

This is a list of pathogenic ClinVar variants found in the PDE7B region.

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

Position	Type	Phenotype	Significance	ClinVar
6-135947468-G-C		not specified	Uncertain significance (Jul 28, 2021)
6-136108803-G-A		not specified	Uncertain significance (May 11, 2022)
6-136147433-G-A			Benign (Jun 27, 2018)
6-136149088-A-G		not specified	Uncertain significance (Oct 26, 2021)
6-136154165-A-C		not specified	Uncertain significance (Jan 10, 2023)
6-136155644-G-A			Benign (Dec 14, 2017)
6-136155659-G-A		not specified	Uncertain significance (Jan 08, 2024)
6-136155723-A-G		not specified	Uncertain significance (Apr 18, 2023)
6-136173827-C-T		Malignant tumor of prostate	Uncertain significance (-)
6-136173836-A-G		not specified	Uncertain significance (Jul 14, 2021)
6-136173860-C-G		not specified	Uncertain significance (Jul 17, 2023)
6-136173871-T-C			Benign (Aug 20, 2018)
6-136179071-G-C		not specified	Uncertain significance (Feb 06, 2023)
6-136179077-A-G			Benign (Jun 27, 2018)
6-136181230-G-T		not specified	Uncertain significance (Oct 05, 2023)
6-136181267-T-G		not specified	Uncertain significance (Jul 19, 2022)
6-136181305-G-C		not specified	Uncertain significance (Dec 28, 2023)
6-136187075-T-C		not specified	Uncertain significance (Dec 06, 2022)
6-136191773-G-A		not specified	Uncertain significance (Nov 17, 2022)
6-136191810-G-C		not specified	Uncertain significance (Dec 08, 2023)
6-136191833-G-A		not specified	Uncertain significance (Sep 20, 2023)
6-136191834-C-G			Benign (May 14, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PDE7B	protein_coding	protein_coding	ENST00000308191	13	343879

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.546	0.454	125725	0	23	125748	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.37	200	262	0.762	0.0000143	3017
Missense in Polyphen		67	109.89	0.60968		1356
Synonymous	0.428	91	96.3	0.945	0.00000576	791
Loss of Function	3.91	6	28.5	0.211	0.00000165	295

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000246	0.000246
Ashkenazi Jewish	0.0000999	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000123	0.000123
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000980	0.0000980
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 the control of cAMP-mediated neural activity and cAMP metabolism in the brain.
• Pathway: Purine metabolism - 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;Purine nucleotides nucleosides metabolism;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.137

Intolerance Scores

• loftool: 0.427
• rvis_EVS: -0.29
• rvis_percentile_EVS: 33.2

Haploinsufficiency Scores

• pHI: 0.483
• hipred: Y
• hipred_score: 0.707
• ghis: 0.516

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.540

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pde7b

Gene ontology

• Biological process: cAMP catabolic process;signal transduction;G protein-coupled receptor signaling pathway;chemical synaptic transmission
• Cellular component: cytosol
• Molecular function: 3',5'-cyclic-AMP phosphodiesterase activity;metal ion binding