PDE1C (phosphodiesterase 1C)

Gene

• Entrez ID: 5137
• Gene name: Phosphodiesterase 1C
• Gene symbol: PDE1C
• Synonyms (NCBI Gene): DFNA74, Hcam3, cam-PDE 1C, hCam-3
• Chromosome: 7
• Chromosome location: 7p14.3
• Summary: This gene encodes an enzyme that belongs to the 3`5`-cyclic nucleotide phosphodiesterase family. Members of this family catalyze hydrolysis of the cyclic nucleotides, cyclic adenosine monophosphate and cyclic guanosine monophosphate, to the corresponding

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs775633137	C>A	Pathogenic, likely-pathogenic	Coding sequence variant, non coding transcript variant, missense variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT1220231	hsa-miR-1253	CLIP-seq
MIRT1220232	hsa-miR-1270	CLIP-seq
MIRT1220233	hsa-miR-3185	CLIP-seq
MIRT1220234	hsa-miR-3190	CLIP-seq
MIRT1220235	hsa-miR-4428	CLIP-seq
MIRT1220236	hsa-miR-4434	CLIP-seq
MIRT1220237	hsa-miR-4516	CLIP-seq
MIRT1220238	hsa-miR-4531	CLIP-seq
MIRT1220239	hsa-miR-4696	CLIP-seq
MIRT1220240	hsa-miR-4766-5p	CLIP-seq
MIRT1220241	hsa-miR-488	CLIP-seq
MIRT1220242	hsa-miR-570	CLIP-seq
MIRT1220243	hsa-miR-620	CLIP-seq
MIRT1220244	hsa-miR-7	CLIP-seq
MIRT1220245	hsa-miR-885-3p	CLIP-seq
MIRT1220246	hsa-miR-1284	CLIP-seq
MIRT1220247	hsa-miR-1303	CLIP-seq
MIRT1220248	hsa-miR-300	CLIP-seq
MIRT1220249	hsa-miR-3144-3p	CLIP-seq
MIRT1220250	hsa-miR-381	CLIP-seq
MIRT1220251	hsa-miR-4666-3p	CLIP-seq
MIRT1220252	hsa-miR-4796-5p	CLIP-seq
MIRT1220253	hsa-miR-1285	CLIP-seq
MIRT1220247	hsa-miR-1303	CLIP-seq
MIRT1220249	hsa-miR-3144-3p	CLIP-seq
MIRT1220254	hsa-miR-3187-5p	CLIP-seq
MIRT1220255	hsa-miR-378g	CLIP-seq
MIRT1220256	hsa-miR-4486	CLIP-seq
MIRT1220257	hsa-miR-612	CLIP-seq
MIRT2063607	hsa-miR-3165	CLIP-seq
MIRT2063608	hsa-miR-5096	CLIP-seq
MIRT2063609	hsa-miR-579	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0004114	Function	3',5'-cyclic-nucleotide phosphodiesterase activity	IEA
GO:0004115	Function	3',5'-cyclic-AMP phosphodiesterase activity	IDA	29860631
GO:0004115	Function	3',5'-cyclic-AMP phosphodiesterase activity	IEA
GO:0004117	Function	Calmodulin-activated dual specificity 3',5'-cyclic-GMP, 3',5'-cyclic-AMP phosphodiesterase activity	IBA
GO:0004117	Function	Calmodulin-activated dual specificity 3',5'-cyclic-GMP, 3',5'-cyclic-AMP phosphodiesterase activity	IDA	8557689
GO:0005516	Function	Calmodulin binding	IEA
GO:0005764	Component	Lysosome	IEA
GO:0005764	Component	Lysosome	ISS
GO:0005829	Component	Cytosol	TAS
GO:0007165	Process	Signal transduction	IEA
GO:0008081	Function	Phosphoric diester hydrolase activity	IEA
GO:0016787	Function	Hydrolase activity	IEA
GO:0043025	Component	Neuronal cell body	IBA
GO:0046872	Function	Metal ion binding	IEA
GO:0047555	Function	3',5'-cyclic-GMP phosphodiesterase activity	IDA	29860631
GO:0047555	Function	3',5'-cyclic-GMP phosphodiesterase activity	IEA
GO:0048101	Function	Calmodulin-activated 3',5'-cyclic-GMP phosphodiesterase activity	IBA
GO:0141162	Process	Negative regulation of cAMP/PKA signal transduction	IBA

Other IDs

• MIM: 602987
• HGNC: 8776
• e!Ensembl: ENSG00000154678

Protein

• UniProt ID: Q14123
• Protein name: Dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1C (Cam-PDE 1C) (EC 3.1.4.17) (Hcam3)
• Protein function: Calmodulin-dependent cyclic nucleotide phosphodiesterase with a dual specificity for the second messengers cAMP and cGMP, which are key regulators of many important physiological processes (PubMed:29860631, PubMed:8557689). Has a high affinity f
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF08499	PDEase_I_N	82 → 142		Family
  PF00233	PDEase_I	227 → 458		Domain

• Tissue specificity: TISSUE SPECIFICITY: Isoform PDE1C2 is present in the heart and brain and, at lower levels in the lung, liver, kidney and skeletal muscle (PubMed:8557689). Isoform PDE1C1 is expressed in the heart and brain and, at lower levels in lung (PubMed:8557689). Al
• Sequence:

  MESPTKEIEEFESNSLKYLQPEQIEKIWLRLRGLRKYKKTSQRLRSLVKQLERGEASVVD
  LKKNLEYAATVLESVYIDETRRLLDTEDELSDIQSDAVPSEVRDWLASTFTRQMGMMLRR
  SDEKPRFKSIVHAVQAGIFVERMYRRTSNMVGLSYPPAVIEALKDVDKWSFDVFSLNEAS
  GDHALKFIFYELLTRYDLISRFKIPISALVSFVEALEVGYSKHKNPYHNLMHAADVTQTV
  HYLLYKTGVANWLTELEIFAIIFSAAIHDYEHTGTTNNFHIQTRSDPAILYNDRSVLENH
  HLSAAYRLLQDDEEMNILINLSKDDWREFRTLVIEMVMATDMSCHFQQIKAMKTALQQPE
  AIEKPKALSLMLHTADISHPAKAWDLHHRWTMSLLEEFFRQGDREAELGLPFSPLCDRKS
  TMVAQSQVGFIDFIVEPTFTVLTDMTEKIVSPLIDETSQTGGTGQRRSSLNSISSSDAKR
  SGVKTSGSEGSAPINNSVISVDYKSFKATWTEVVHINRERWRAKVPKEEKAKKEAEEKAR
  LAAEEQQKEMEAKSQAEEGASGKAEKKTSGETKNQVNGTRANKSDNPRGKNSKAEKSSGE
  QQQNGDFKDGKNKTDKKDHSNIGNDSKKTDGTKQRSHGSPAPSTSSTCRLTLPVIKPPLR
  HFKRPAYASSSYAPSVSKKTDEHPARYKMLDQRIKMKKIQNISHNWNRK

• Sequence length: 709

Pathways

KEGG:

Purine metabolism
Metabolic pathways
Calcium signaling pathway
Olfactory transduction
Taste transduction
Renin secretion
Morphine addiction

Reactome:

Cam-PDE 1 activation

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Autosomal dominant nonsyndromic hearing loss	Likely pathogenic; Pathogenic	rs775633137	RCV000590894	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Hearing loss, autosomal dominant 74	Likely pathogenic; Pathogenic	rs2534865414, rs368406121, rs775633137	RCV004585125 RCV004585126 RCV000690972	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Acute myeloid leukemia	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ASTROCYTOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ATTENTION DEFICIT HYPERACTIVITY DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
AUTISM SPECTRUM DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
AUTOSOMAL DOMINANT ISOLATED SENSORINEURAL DEAFNESS TYPE DFNA	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CENTRAL NERVOUS SYSTEM CANCER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Clear cell carcinoma of kidney	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COLORECTAL CANCER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CORNEAL NEOVASCULARIZATION	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CORONARY ARTERY DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DEAFNESS, AUTOSOMAL DOMINANT 74	—	Disgenet, HPO Disgenet, HPO	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DRY EYE SYNDROME	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
EBV-positive nodal T- and NK-cell lymphoma	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ENDOMETRIOSIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
FEMALE REPRODUCTIVE SYSTEM DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GASTROESOPHAGEAL REFLUX DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GLIOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GOUT	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HYPERCHOLESTEROLEMIA	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HYPERLIPOPROTEINEMIA TYPE IIA	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INSOMNIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
KERATITIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
METABOLIC SYNDROME	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MOYAMOYA DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NEUROTIC DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NON-ALCOHOLIC FATTY LIVER DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Nonpapillary renal cell carcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PDE1C-related disorder	Benign; Uncertain significance; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Prostate cancer	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCHIZOPHRENIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCOLIOSIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SMOOTH SURFACE DENTAL CARIES	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SUBSTANCE ABUSE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TYPE 2 DIABETES MELLITUS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine carcinosarcoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Amyotrophic lateral sclerosis 1	Amyotrophic lateral sclerosis	Pubtator	35853630	Associate	★☆☆☆☆ Found in Text Mining only
Arthritis, Gouty	Gouty arthritis	GWASCAT_DG	22179738		★☆☆☆☆ Found in Text Mining only
Asthenozoospermia	Asthenozoospermia	Pubtator	27232852	Associate	★☆☆☆☆ Found in Text Mining only
Autosomal dominant non-syndromic sensorineural deafness type DFNA	Non-Syndromic Sensorineural Deafness	Orphanet			★☆☆☆☆ Found in Text Mining only
Cardiomyopathy, Familial Idiopathic	Cardiomyopathy	BEFREE	27427220		★☆☆☆☆ Found in Text Mining only
CNS disorder	CNS Disorder	BEFREE	30800055		★☆☆☆☆ Found in Text Mining only
Congestive heart failure	Congestive Heart Failure	BEFREE	30030415		★☆☆☆☆ Found in Text Mining only
DEAFNESS, AUTOSOMAL DOMINANT 74	Deafness	UNIPROT_DG	29860631		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Degenerative polyarthritis	Arthritis	GWASDB_DG	22763110		★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus Type 2	Diabetes mellitus, type 2	Pubtator	38137029	Associate	★☆☆☆☆ Found in Text Mining only
Endometriosis	Endometriosis	GWASDB_DG	23472165		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Endometriosis	Endometriosis	GWASCAT_DG	23472165		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial Primary Pulmonary Hypertension	Pulmonary hypertension	Pubtator	16980375	Stimulate	★☆☆☆☆ Found in Text Mining only
Glioblastoma	Glioblastoma	BEFREE	17697115, 25620587		★☆☆☆☆ Found in Text Mining only
Glioblastoma Multiforme	Glioblastoma	BEFREE	17697115, 25620587		★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	BEFREE	23664928		★☆☆☆☆ Found in Text Mining only
Gout	Gout	GWASCAT_DG	22179738		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Heart failure	Heart Failure	BEFREE	30030415		★☆☆☆☆ Found in Text Mining only
Hypertension Pulmonary	Pulmonary hypertension	Pubtator	16980375	Associate	★☆☆☆☆ Found in Text Mining only
melanoma	Melanoma	BEFREE	19414353, 27344179		★☆☆☆☆ Found in Text Mining only
Melanoma	Melanoma	Pubtator	19414353, 27344179	Associate	★☆☆☆☆ Found in Text Mining only
Myopia	Myopia	Pubtator	34241624	Associate	★☆☆☆☆ Found in Text Mining only
Nonsyndromic Deafness	Nonsyndromic Deafness	BEFREE	29860631		★☆☆☆☆ Found in Text Mining only