PDE1A
Basic information
Region (hg38): 2:182139968-182523359
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (51 variants)
- not_provided (7 variants)
- PDE1A-related_disorder (2 variants)
- EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)
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. These statistics are base on transcript: NM_001363871.4. 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 | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 2 | |||||
missense | 49 | 51 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 49 | 4 | 0 |
GnomAD
Source:
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:
- 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
- essential_gene_gene_trap
- 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
- Phenotype
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