PDE7A

phosphodiesterase 7A, the group of Phosphodiesterases

Basic information

Region (hg38): 8:65714334-65842322

Links

ENSG00000205268 ∙ NCBI:5150 ∙ OMIM:171885 ∙ HGNC:8791 ∙ Uniprot:Q13946 ∙ 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 PDE7A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDE7A 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						0
missense			20			20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	0	0

Variants in PDE7A

This is a list of pathogenic ClinVar variants found in the PDE7A region.

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

Position	Type	Phenotype	Significance	ClinVar
8-65719297-A-G		not specified	Uncertain significance (Mar 01, 2024)
8-65719312-G-A		not specified	Uncertain significance (Apr 07, 2022)
8-65719340-C-T		not specified	Uncertain significance (Dec 13, 2023)
8-65719342-G-T		not specified	Uncertain significance (Oct 04, 2022)
8-65719463-T-C		not specified	Uncertain significance (May 03, 2023)
8-65719472-G-C		not specified	Uncertain significance (Jan 26, 2022)
8-65719472-G-T		not specified	Uncertain significance (Apr 25, 2023)
8-65723570-T-C		not specified	Uncertain significance (May 17, 2023)
8-65723571-G-A		not specified	Uncertain significance (Feb 10, 2022)
8-65723573-C-T		not specified	Uncertain significance (Apr 10, 2023)
8-65723574-G-A		not specified	Uncertain significance (Jun 07, 2022)
8-65723585-G-A		not specified	Uncertain significance (Feb 14, 2023)
8-65723604-A-T		not specified	Uncertain significance (Apr 13, 2022)
8-65724348-C-T		not specified	Uncertain significance (Nov 30, 2021)
8-65724914-T-C		not specified	Uncertain significance (Nov 14, 2023)
8-65734862-G-A		not specified	Uncertain significance (Jan 02, 2024)
8-65734889-T-C		not specified	Uncertain significance (Dec 02, 2022)
8-65739576-G-A		not specified	Uncertain significance (Oct 03, 2022)
8-65745437-C-G		not specified	Uncertain significance (Jan 23, 2023)
8-65747729-A-T		not specified	Uncertain significance (Oct 26, 2022)
8-65779747-G-A		not specified	Uncertain significance (May 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PDE7A	protein_coding	protein_coding	ENST00000401827	13	124813

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00456	0.995	125732	0	14	125746	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.72	176	253	0.696	0.0000134	3153
Missense in Polyphen		60	109.61	0.5474		1445
Synonymous	0.794	81	90.6	0.894	0.00000473	881
Loss of Function	3.19	9	26.8	0.335	0.00000131	334

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
Ashkenazi Jewish	0.00	0.00
East Asian	0.000118	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000717	0.0000703
Middle Eastern	0.000118	0.000109
South Asian	0.0000349	0.0000327
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 have a role in muscle signal transduction. {ECO:0000269|PubMed:19350606}.
• Pathway: Purine metabolism - Homo sapiens (human);Morphine addiction - Homo sapiens (human);Ectoderm Differentiation;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: 0.146

Intolerance Scores

• loftool: 0.428
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.91

Haploinsufficiency Scores

• pHI: 0.636
• hipred: Y
• hipred_score: 0.506
• ghis: 0.597

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: K
• gene_indispensability_pred: E
• gene_indispensability_score: 0.510

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pde7a
• Phenotype: immune system phenotype

Gene ontology

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