PDE5A

phosphodiesterase 5A, the group of Phosphodiesterases

Basic information

Region (hg38): 4:119494397-119628804

Links

ENSG00000138735 ∙ NCBI:8654 ∙ OMIM:603310 ∙ HGNC:8784 ∙ Uniprot:O76074 ∙ 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 PDE5A gene.

• not_specified (76 variants)
• not_provided (15 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDE5A gene is commonly pathogenic or not. These statistics are base on transcript: NM_000001083.4. 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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				5	3	8
missense			72	5	2	79
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	72	10	5

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PDE5A	protein_coding	protein_coding	ENST00000354960	21	134597

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000106	1.00	125701	0	47	125748	0.000187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.10	327	453	0.722	0.0000224	5828
Missense in Polyphen		96	169.63	0.56595		2206
Synonymous	1.33	136	157	0.865	0.00000777	1532
Loss of Function	4.25	16	47.6	0.336	0.00000235	588

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000489	0.000460
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000163	0.000163
Finnish	0.000232	0.000231
European (Non-Finnish)	0.000216	0.000211
Middle Eastern	0.000163	0.000163
South Asian	0.000113	0.0000980
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in signal transduction by regulating the intracellular concentration of cyclic nucleotides. This phosphodiesterase catalyzes the specific hydrolysis of cGMP to 5'- GMP (PubMed:9714779, PubMed:15489334). Specifically regulates nitric-oxide-generated cGMP (PubMed:15489334). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9714779}.
• Pathway: Purine metabolism - Homo sapiens (human);cGMP-PKG signaling pathway - Homo sapiens (human);Phosphodiesterases in neuronal function;Purine nucleotides nucleosides metabolism;Hemostasis;cGMP effects;Nitric oxide stimulates guanylate cyclase;Platelet homeostasis (Consensus)

Recessive Scores

• pRec: 0.238

Intolerance Scores

• loftool: 0.457
• rvis_EVS: 1.05
• rvis_percentile_EVS: 91.34

Haploinsufficiency Scores

• pHI: 0.178
• hipred: Y
• hipred_score: 0.641
• ghis: 0.475

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.443

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pde5a

Gene ontology

• Biological process: signal transduction;positive regulation of cardiac muscle hypertrophy;regulation of nitric oxide mediated signal transduction;negative regulation of T cell proliferation;positive regulation of MAP kinase activity;cGMP catabolic process;negative regulation of cardiac muscle contraction;relaxation of cardiac muscle;positive regulation of oocyte development
• Cellular component: cellular_component;cytosol
• Molecular function: 3',5'-cyclic-nucleotide phosphodiesterase activity;protein binding;cGMP binding;metal ion binding;3',5'-cyclic-GMP phosphodiesterase activity