PDE12

phosphodiesterase 12

Basic information

Region (hg38): 3:57556274-57656480

Links

ENSG00000174840 ∙ NCBI:201626 ∙ OMIM:616519 ∙ HGNC:25386 ∙ Uniprot:Q6L8Q7 ∙ 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 PDE12 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDE12 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			32	1		33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	32	1	0

Variants in PDE12

This is a list of pathogenic ClinVar variants found in the PDE12 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-57556410-C-T		not specified	Uncertain significance (Jun 05, 2023)
3-57556480-C-T		not specified	Uncertain significance (Oct 29, 2021)
3-57556506-G-C		not specified	Uncertain significance (May 08, 2024)
3-57556561-A-G		not specified	Uncertain significance (Jan 17, 2024)
3-57556566-A-G		not specified	Uncertain significance (May 24, 2023)
3-57556585-A-C		not specified	Uncertain significance (Nov 30, 2022)
3-57556614-G-A		not specified	Uncertain significance (Feb 14, 2024)
3-57556621-A-G		not specified	Uncertain significance (Apr 26, 2023)
3-57556632-G-A		not specified	Uncertain significance (Feb 27, 2024)
3-57556660-A-G		not specified	Uncertain significance (Feb 01, 2023)
3-57556758-T-G		not specified	Uncertain significance (Dec 20, 2023)
3-57556761-C-G		not specified	Uncertain significance (Nov 02, 2023)
3-57556878-C-G		not specified	Uncertain significance (Feb 27, 2024)
3-57556882-A-G		not specified	Uncertain significance (Dec 03, 2021)
3-57556894-A-G		not specified	Uncertain significance (Aug 11, 2022)
3-57557083-A-G		not specified	Uncertain significance (Feb 28, 2024)
3-57557107-G-C		not specified	Uncertain significance (Jan 31, 2024)
3-57557139-G-A		not specified	Likely benign (Dec 27, 2023)
3-57557212-C-A		not specified	Uncertain significance (Mar 16, 2022)
3-57557312-G-T		not specified	Uncertain significance (Sep 16, 2021)
3-57557343-G-C		not specified	Uncertain significance (May 08, 2023)
3-57557374-A-G		not specified	Uncertain significance (Nov 10, 2021)
3-57557464-T-G		not specified	Uncertain significance (May 09, 2022)
3-57557556-C-T		not specified	Uncertain significance (Feb 06, 2024)
3-57557590-C-T		not specified	Uncertain significance (Feb 27, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PDE12	protein_coding	protein_coding	ENST00000311180	3	10569

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0444	0.955	125722	0	26	125748	0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.40	268	340	0.787	0.0000159	3947
Missense in Polyphen		51	71.491	0.71338		837
Synonymous	0.818	130	142	0.913	0.00000696	1268
Loss of Function	2.87	6	19.8	0.303	9.02e-7	240

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000252	0.000242
Ashkenazi Jewish	0.000102	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000133	0.000132
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Enzyme that cleaves 2',5'-phosphodiester bond linking adenosines of the 5'-triphosphorylated oligoadenylates, triphosphorylated oligoadenylates referred as 2-5A modulates the 2-5A system. This enzyme degraded triphosphorylated 2-5A to produce AMP and ATP. Also cleaves 3',5'-phosphodiester bond of oligoadenylates. Plays a role as a negative regulator of the The 2-5A system that is one of the major pathways for antiviral and antitumor functions induced by interferons (IFNs). Suppression of this enzyme induces reduction of viral replication in Hela cells, thus counteracting the antiviral pathway probably by inhibiting the 2-5A system. {ECO:0000269|PubMed:15231837, ECO:0000269|PubMed:21245038, ECO:0000269|PubMed:21666256, ECO:0000269|PubMed:22285541}.
• Pathway: Phosphodiesterases in neuronal function (Consensus)

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.403
• rvis_EVS: -0.18
• rvis_percentile_EVS: 40.36

Haploinsufficiency Scores

• pHI: 0.0844
• hipred: N
• hipred_score: 0.463
• ghis: 0.644

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.850

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pde12
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan)

Gene ontology

• Biological process: nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay;mitochondrial mRNA catabolic process;mRNA processing;cellular response to interferon-alpha;regulation of mitochondrial mRNA stability;positive regulation of viral genome replication;defense response to virus;negative regulation of cell death;cellular response to interferon-gamma;cellular response to dsRNA;nucleic acid phosphodiester bond hydrolysis;negative regulation of oxidative phosphorylation;RNA phosphodiester bond hydrolysis, exonucleolytic
• Cellular component: mitochondrial matrix;cytosol
• Molecular function: 3'-5'-exoribonuclease activity;exonuclease activity;poly(A)-specific ribonuclease activity;oligoribonucleotidase activity;metal ion binding