DAPK3
death associated protein kinase 3, the group of Death associated protein kinases|MicroRNA protein coding host genes
Basic information
Region (hg38): 19:3958453-3971123
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (66 variants)
- not_provided (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the DAPK3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000001348.3. 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 | 65 | 65 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 65 | 1 | 1 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| DAPK3 | protein_coding | protein_coding | ENST00000545797 | 8 | 12671 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00655 | 0.990 | 125712 | 0 | 28 | 125740 | 0.000111 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.80 | 239 | 331 | 0.722 | 0.0000260 | 2916 |
| Missense in Polyphen | 47 | 98.959 | 0.47494 | 979 | ||
| Synonymous | -0.909 | 160 | 146 | 1.10 | 0.0000120 | 879 |
| Loss of Function | 2.55 | 7 | 19.0 | 0.368 | 9.10e-7 | 221 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000216 | 0.000214 |
| Ashkenazi Jewish | 0.000202 | 0.000198 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.000142 | 0.000139 |
| European (Non-Finnish) | 0.000135 | 0.000132 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.000131 | 0.000131 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Serine/threonine kinase which is involved in the regulation of apoptosis, autophagy, transcription, translation and actin cytoskeleton reorganization. Involved in the regulation of smooth muscle contraction. Regulates both type I (caspase- dependent) apoptotic and type II (caspase-independent) autophagic cell deaths signal, depending on the cellular setting. Involved in regulation of starvation-induced autophagy. Regulates myosin phosphorylation in both smooth muscle and non-muscle cells. In smooth muscle, regulates myosin either directly by phosphorylating MYL12B and MYL9 or through inhibition of smooth muscle myosin phosphatase (SMPP1M) via phosphorylation of PPP1R12A; the inhibition of SMPP1M functions to enhance muscle responsiveness to Ca(2+) and promote a contractile state. Phosphorylates MYL12B in non-muscle cells leading to reorganization of actin cytoskeleton. Isoform 2 can phosphorylate myosin, PPP1R12A and MYL12B. Overexpression leads to condensation of actin stress fibers into thick bundles. Involved in actin filament focal adhesion dynamics. The function in both reorganization of actin cytoskeleton and focal adhesion dissolution is modulated by RhoD. Positively regulates canonical Wnt/beta-catenin signaling through interaction with NLK and TCF7L2. Phosphorylates RPL13A on 'Ser-77' upon interferon-gamma activation which is causing RPL13A release from the ribosome, RPL13A association with the GAIT complex and its subsequent involvement in transcript-selective translation inhibition. Enhances transcription from AR-responsive promoters in a hormone- and kinase-dependent manner. Involved in regulation of cell cycle progression and cell proliferation. May be a tumor suppressor. {ECO:0000269|PubMed:10356987, ECO:0000269|PubMed:11384979, ECO:0000269|PubMed:11781833, ECO:0000269|PubMed:12917339, ECO:0000269|PubMed:15096528, ECO:0000269|PubMed:15367680, ECO:0000269|PubMed:16219639, ECO:0000269|PubMed:17126281, ECO:0000269|PubMed:17158456, ECO:0000269|PubMed:18084323, ECO:0000269|PubMed:18995835, ECO:0000269|PubMed:21169990, ECO:0000269|PubMed:21408167, ECO:0000269|PubMed:21454679, ECO:0000269|PubMed:21487036, ECO:0000269|PubMed:23454120}.;
- Pathway
- Bladder cancer - Homo sapiens (human);Autophagy - animal - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Bladder Cancer;Caspase activation via extrinsic apoptotic signalling pathway;Apoptosis;Programmed Cell Death;AndrogenReceptor;Ligand-independent caspase activation via DCC
(Consensus)
Recessive Scores
- pRec
- 0.258
Intolerance Scores
- loftool
- rvis_EVS
- -0.78
- rvis_percentile_EVS
- 12.77
Haploinsufficiency Scores
- pHI
- 0.139
- hipred
- Y
- hipred_score
- 0.800
- ghis
- 0.654
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.916
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Dapk3
- Phenotype
- normal 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); embryo phenotype;
Gene ontology
- Biological process
- chromatin organization;regulation of transcription, DNA-templated;protein phosphorylation;apoptotic process;regulation of smooth muscle contraction;regulation of mitotic nuclear division;regulation of mitotic cell cycle;regulation of cell shape;regulation of autophagy;negative regulation of translation;neuron differentiation;positive regulation of cell migration;intracellular signal transduction;regulation of apoptotic process;positive regulation of apoptotic process;regulation of myosin II filament organization;protein autophosphorylation;regulation of focal adhesion assembly;cellular response to interferon-gamma;positive regulation of canonical Wnt signaling pathway;apoptotic signaling pathway;regulation of cell motility;regulation of actin cytoskeleton reorganization;positive regulation of extrinsic apoptotic signaling pathway in absence of ligand
- Cellular component
- nucleus;cytoplasm;actin filament;PML body;membrane raft
- Molecular function
- protein serine/threonine kinase activity;protein binding;ATP binding;protein C-terminus binding;cAMP response element binding protein binding;Rho GTPase binding;identical protein binding;protein homodimerization activity;leucine zipper domain binding