DAPK2

death associated protein kinase 2, the group of Death associated protein kinases

Basic information

Region (hg38): 15:63907035-64072033

Links

ENSG00000035664 ∙ NCBI:23604 ∙ OMIM:616567 ∙ HGNC:2675 ∙ Uniprot:Q9UIK4 ∙ 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 DAPK2 gene.

• Inborn genetic diseases (19 variants)
• not provided (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DAPK2 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	2
missense			19	2		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	2	3
non coding						0
Total	0	0	19	3	1

Variants in DAPK2

This is a list of pathogenic ClinVar variants found in the DAPK2 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-63908535-C-T			Benign (Apr 20, 2018)
15-63908578-T-A		not specified	Uncertain significance (Dec 14, 2021)
15-63908591-C-T		not specified	Uncertain significance (Jan 24, 2024)
15-63911934-C-T		not specified	Uncertain significance (Jul 09, 2021)
15-63911948-G-A		not specified	Uncertain significance (Jan 17, 2024)
15-63911948-G-C		not specified	Uncertain significance (Sep 17, 2021)
15-63911967-A-G		not specified	Uncertain significance (Mar 07, 2024)
15-63911972-G-T		not specified	Uncertain significance (Sep 26, 2023)
15-63912116-G-A		not specified	Uncertain significance (Mar 14, 2023)
15-63912122-G-A		not specified	Uncertain significance (May 01, 2023)
15-63912125-C-T		not specified	Uncertain significance (Nov 07, 2022)
15-63912195-C-T			Benign (Mar 07, 2018)
15-63924827-G-A		not specified	Uncertain significance (Aug 12, 2021)
15-63924856-C-T		not specified	Uncertain significance (Feb 21, 2024)
15-63925942-G-A		not specified	Uncertain significance (Feb 17, 2024)
15-63925943-G-A			Benign (Aug 18, 2018)
15-63925974-T-A		not specified	Uncertain significance (May 10, 2022)
15-63925985-C-G		not specified	Uncertain significance (Feb 06, 2023)
15-63926086-C-T		not specified	Uncertain significance (Dec 05, 2022)
15-63930399-C-A			Benign/Likely benign (Mar 01, 2023)
15-63971425-T-G		not specified	Uncertain significance (Feb 28, 2023)
15-63971452-T-G		not specified	Uncertain significance (Dec 06, 2021)
15-63971471-A-C		not specified	Uncertain significance (Feb 23, 2023)
15-63971499-G-A		not specified	Uncertain significance (Nov 14, 2023)
15-63971539-C-T		not specified	Uncertain significance (Aug 10, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DAPK2	protein_coding	protein_coding	ENST00000261891	11	164998

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.01e-10	0.213	125713	0	35	125748	0.000139

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.352	215	230	0.935	0.0000147	2453
Missense in Polyphen		72	81.902	0.8791		825
Synonymous	0.103	90	91.3	0.986	0.00000601	679
Loss of Function	0.633	16	19.0	0.843	8.04e-7	231

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000174	0.000174
Ashkenazi Jewish	0.00	0.00
East Asian	0.000336	0.000272
Finnish	0.0000490	0.0000462
European (Non-Finnish)	0.000159	0.000158
Middle Eastern	0.000336	0.000272
South Asian	0.000131	0.000131
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Calcium/calmodulin-dependent serine/threonine kinase involved in multiple cellular signaling pathways that trigger cell survival, apoptosis, and autophagy. Regulates both type I apoptotic and type II autophagic cell death signals, depending on the cellular setting. The former is caspase-dependent, while the latter is caspase-independent and is characterized by the accumulation of autophagic vesicles. Acts as a mediator of anoikis and a suppressor of beta-catenin-dependent anchorage-independent growth of malignant epithelial cells. May play a role in granulocytic maturation (PubMed:17347302). Regulates granulocytic motility by controlling cell spreading and polarization (PubMed:24163421). {ECO:0000269|PubMed:17347302, ECO:0000269|PubMed:24163421, ECO:0000269|PubMed:26047703}.
• 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;Ligand-independent caspase activation via DCC (Consensus)

Recessive Scores

• pRec: 0.129

Intolerance Scores

• loftool: 0.742
• rvis_EVS: 0.09
• rvis_percentile_EVS: 60.47

Haploinsufficiency Scores

• pHI: 0.441
• hipred: N
• hipred_score: 0.350
• ghis: 0.449

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.824

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dapk2
• Phenotype: homeostasis/metabolism phenotype; immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: protein phosphorylation;apoptotic process;regulation of autophagy;intracellular signal transduction;regulation of apoptotic process;anoikis;protein autophosphorylation;positive regulation of neutrophil chemotaxis;neutrophil migration;positive regulation of eosinophil chemotaxis;regulation of intrinsic apoptotic signaling pathway
• Cellular component: nucleus;cytoplasm;Golgi apparatus;cytoplasmic vesicle;autophagosome lumen;intracellular membrane-bounded organelle
• Molecular function: protein serine/threonine kinase activity;protein binding;calmodulin binding;ATP binding;identical protein binding