PDE1A

phosphodiesterase 1A, the group of Phosphodiesterases

Basic information

Region (hg38): 2:182139968-182523359

Links

ENSG00000115252 ∙ ∙ OMIM:171890 ∙ HGNC:8774 ∙ Uniprot:P54750 ∙ 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 PDE1A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDE1A 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			22	2		24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					2	2
non coding				1	29	30
Total	0	0	22	3	29

Variants in PDE1A

This is a list of pathogenic ClinVar variants found in the PDE1A region.

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

Position	Type	Phenotype	Significance	ClinVar
2-182147146-G-A		not specified	Uncertain significance (Sep 21, 2023)
2-182168051-T-C			Benign (May 14, 2021)
2-182168293-GA-G			Benign (May 14, 2021)
2-182168475-A-G			Benign (May 14, 2021)
2-182185900-G-T		not specified	Uncertain significance (Nov 06, 2023)
2-182185955-T-G		not specified	Uncertain significance (Jun 29, 2023)
2-182185973-C-T		not specified	Uncertain significance (Jan 03, 2024)
2-182186054-T-C		not specified	Likely benign (May 26, 2023)
2-182186068-A-G		not specified	Uncertain significance (Jun 28, 2022)
2-182186075-T-C		not specified	Uncertain significance (Feb 10, 2022)
2-182186236-C-G			Benign (May 14, 2021)
2-182186483-G-A		not specified	Uncertain significance (Mar 27, 2023)
2-182186520-G-A		not specified	Uncertain significance (Feb 22, 2023)
2-182186572-T-C		not specified	Uncertain significance (Nov 22, 2023)
2-182186694-A-G			Benign (May 13, 2021)
2-182186722-T-C			Benign (May 14, 2021)
2-182188917-T-A			Benign (May 14, 2021)
2-182188931-C-G			Benign (May 13, 2021)
2-182201650-C-CA			Benign (May 13, 2021)
2-182201650-C-CAA			Benign (May 15, 2021)
2-182201650-C-CAAA			Benign (May 13, 2021)
2-182201650-C-CAAAAA			Benign (May 22, 2021)
2-182201650-C-CAAAAAA			Benign (May 31, 2021)
2-182201664-C-A			Benign (May 13, 2021)
2-182201710-T-C		not specified	Uncertain significance (Jun 22, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PDE1A	protein_coding	protein_coding	ENST00000435564	14	383157

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0135	0.986	125725	1	17	125743	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.967	246	293	0.841	0.0000150	3587
Missense in Polyphen		91	130.4	0.69785		1619
Synonymous	-0.375	106	101	1.05	0.00000521	996
Loss of Function	3.53	9	29.8	0.302	0.00000148	376

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.000172	0.000163
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.0000626	0.0000615
Middle Eastern	0.000172	0.000163
South Asian	0.000197	0.000163
Other	0.000167	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 higher affinity for cGMP than for cAMP.
• 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: 0.201

Intolerance Scores

• loftool: 0.376
• rvis_EVS: -0.73
• rvis_percentile_EVS: 14.02

Haploinsufficiency Scores

• pHI: 0.225
• hipred: Y
• hipred_score: 0.546
• ghis: 0.611

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.561

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pde1a

Zebrafish Information Network

• Gene name: pde1a
• Affected structure: pronephric tubule
• Phenotype tag: abnormal
• Phenotype quality: dilated

Gene ontology

• Biological process: G protein-coupled receptor signaling pathway;regulation of smooth muscle cell apoptotic process;cGMP catabolic process;regulation of smooth muscle cell proliferation
• Cellular component: nucleus;cytosol;neuronal cell body
• Molecular function: 3',5'-cyclic-AMP phosphodiesterase activity;calmodulin-dependent cyclic-nucleotide phosphodiesterase activity;calmodulin binding;metal ion binding;3',5'-cyclic-GMP phosphodiesterase activity;calcium- and calmodulin-regulated 3',5'-cyclic-GMP phosphodiesterase activity