PDE4C

phosphodiesterase 4C, the group of Phosphodiesterases

Basic information

Region (hg38): 19:18207965-18248200

Previous symbols: [ "DPDE1" ]

Links

ENSG00000105650 ∙ NCBI:5143 ∙ OMIM:600128 ∙ HGNC:8782 ∙ Uniprot:Q08493 ∙ 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 PDE4C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDE4C 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				2		2
missense			44	2	2	48
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	44	4	2

Variants in PDE4C

This is a list of pathogenic ClinVar variants found in the PDE4C region.

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

Position	Type	Phenotype	Significance	ClinVar
19-18210947-G-A			Likely benign (Aug 01, 2022)
19-18210994-C-G		not specified	Uncertain significance (Jul 14, 2021)
19-18210996-G-C		not specified	Uncertain significance (Jun 16, 2023)
19-18211054-C-T		not specified	Uncertain significance (Feb 13, 2025)
19-18211090-G-T		not specified	Uncertain significance (Jan 31, 2024)
19-18211108-C-G		not specified	Uncertain significance (Feb 22, 2025)
19-18211120-G-A		not specified	Likely benign (Nov 21, 2023)
19-18211153-G-T		not specified	Uncertain significance (Jul 14, 2021)
19-18211164-T-C		not specified	Uncertain significance (May 27, 2022)
19-18211254-G-A		not specified	Uncertain significance (Mar 18, 2024)
19-18211266-A-G		not specified	Uncertain significance (Mar 01, 2024)
19-18211267-T-C		not specified	Uncertain significance (Nov 30, 2022)
19-18211761-G-C		not specified	Uncertain significance (Mar 05, 2025)
19-18211814-C-A		not specified	Uncertain significance (Sep 13, 2023)
19-18211877-C-T		not specified	Uncertain significance (Apr 05, 2023)
19-18211880-T-C		not specified	Uncertain significance (Jan 18, 2025)
19-18213406-C-T		not specified	Uncertain significance (Jul 26, 2021)
19-18216749-T-C		not specified	Uncertain significance (Jul 02, 2024)
19-18216803-C-T		not specified	Uncertain significance (May 09, 2024)
19-18216838-G-A		not specified	Uncertain significance (Jan 23, 2024)
19-18216849-G-T		not specified	Uncertain significance (Sep 06, 2022)
19-18216877-A-G		not specified	Uncertain significance (Feb 09, 2023)
19-18216878-T-C		not specified	Uncertain significance (Sep 25, 2023)
19-18218153-G-C		not specified	Uncertain significance (Jul 26, 2021)
19-18218217-G-A		not specified	Uncertain significance (Nov 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PDE4C	protein_coding	protein_coding	ENST00000355502	15	47459

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.48e-7	0.991	125685	1	62	125748	0.000251

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.41	344	426	0.807	0.0000256	4609
Missense in Polyphen		123	152.57	0.80617		1642
Synonymous	1.25	168	190	0.885	0.0000125	1451
Loss of Function	2.38	16	30.1	0.532	0.00000145	333

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000848	0.000814
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000292	0.000290
Middle Eastern	0.0000544	0.0000544
South Asian	0.000387	0.000327
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. {ECO:0000269|PubMed:17727341}.
• Pathway: cAMP signaling pathway - Homo sapiens (human);Purine metabolism - Homo sapiens (human);Morphine addiction - Homo sapiens (human);Beta-agonist/Beta-blocker Pathway, Pharmacodynamics;G Protein Signaling Pathways;Phosphodiesterases in neuronal function;Signaling by GPCR;Signal Transduction;G alpha (s) signalling events;DARPP-32 events;Purine nucleotides nucleosides metabolism;Opioid Signalling;G alpha (i) signalling events;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.174

Intolerance Scores

• loftool: 0.417
• rvis_EVS: 0.42
• rvis_percentile_EVS: 77.26

Haploinsufficiency Scores

• pHI: 0.154
• hipred: Y
• hipred_score: 0.522
• ghis: 0.437

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.775

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pde4c

Gene ontology

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