DAPK3

death associated protein kinase 3, the group of Death associated protein kinases|MicroRNA protein coding host genes

Basic information

Region (hg38): 19:3958452-3971123

Links

ENSG00000167657 ∙ NCBI:1613 ∙ OMIM:603289 ∙ HGNC:2676 ∙ Uniprot:O43293 ∙ 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 DAPK3 gene.

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.

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					1	1
missense			20			20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	0	1

Variants in DAPK3

This is a list of pathogenic ClinVar variants found in the DAPK3 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-3959138-T-C		not specified	Uncertain significance (Dec 28, 2023)
19-3959154-C-T		not specified	Uncertain significance (Apr 22, 2024)
19-3959231-C-A		not specified	Uncertain significance (Mar 31, 2023)
19-3959232-G-T		not specified	Uncertain significance (Mar 23, 2022)
19-3959244-C-A		not specified	Uncertain significance (Aug 30, 2021)
19-3959273-T-G		not specified	Uncertain significance (Oct 20, 2021)
19-3959283-C-G		not specified	Uncertain significance (Dec 15, 2023)
19-3959297-G-A		not specified	Uncertain significance (Feb 15, 2023)
19-3959330-C-G		not specified	Uncertain significance (Aug 13, 2021)
19-3959348-C-T		not specified	Uncertain significance (Dec 26, 2023)
19-3959381-T-G		not specified	Uncertain significance (Nov 08, 2021)
19-3959415-C-T		not specified	Uncertain significance (Aug 28, 2023)
19-3959471-G-T		not specified	Uncertain significance (Jun 18, 2021)
19-3959484-C-T		not specified	Uncertain significance (Mar 25, 2024)
19-3959489-G-A		not specified	Uncertain significance (Dec 19, 2022)
19-3959564-C-T		not specified	Uncertain significance (May 08, 2024)
19-3959589-C-G		not specified	Uncertain significance (Feb 16, 2023)
19-3959600-C-T		not specified	Uncertain significance (Feb 06, 2024)
19-3959602-G-C		not specified	Uncertain significance (May 23, 2024)
19-3961033-C-A		not specified	Uncertain significance (Feb 21, 2024)
19-3963665-T-C		not specified	Uncertain significance (Apr 19, 2024)
19-3963879-C-T			Benign (May 25, 2018)
19-3963896-G-A		not specified	Uncertain significance (Mar 28, 2024)
19-3964288-G-A		not specified	Uncertain significance (Apr 01, 2024)
19-3964653-C-T		not specified	Uncertain significance (May 13, 2024)

GnomAD

Source: gnomAD

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: dbNSFP

• 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

• 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