DCLK2

doublecortin like kinase 2, the group of Doublecortin superfamily

Basic information

Region (hg38): 4:150078444-150257438

Previous symbols: [ "DCAMKL2" ]

Links

ENSG00000170390 ∙ NCBI:166614 ∙ OMIM:613166 ∙ HGNC:19002 ∙ Uniprot:Q8N568 ∙ 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 DCLK2 gene.

• Inborn genetic diseases (22 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DCLK2 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				2		2
missense			20	2		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	20	4	0

Variants in DCLK2

This is a list of pathogenic ClinVar variants found in the DCLK2 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-150079041-G-A		not specified	Uncertain significance (May 16, 2023)
4-150079071-G-C		not specified	Uncertain significance (Mar 21, 2023)
4-150079090-G-C			Likely benign (May 01, 2022)
4-150079163-C-A		not specified	Uncertain significance (Jul 19, 2022)
4-150079324-C-G		not specified	Uncertain significance (Nov 09, 2021)
4-150079327-T-G		not specified	Uncertain significance (Apr 28, 2022)
4-150079377-C-T		not specified	Uncertain significance (Nov 09, 2022)
4-150102774-G-A		not specified	Uncertain significance (Sep 27, 2022)
4-150102780-G-A		not specified	Uncertain significance (Jan 23, 2024)
4-150193178-T-G		not specified	Uncertain significance (Jul 19, 2022)
4-150193186-T-C		not specified	Uncertain significance (Oct 13, 2023)
4-150193214-A-G		not specified	Uncertain significance (Nov 21, 2023)
4-150198082-C-A		not specified	Uncertain significance (Aug 02, 2023)
4-150198083-G-A		not specified	Uncertain significance (Jun 23, 2023)
4-150203821-T-C		not specified	Uncertain significance (Dec 12, 2022)
4-150203875-T-C		not specified	Uncertain significance (Dec 21, 2023)
4-150221780-A-G		not specified	Likely benign (May 17, 2023)
4-150224502-T-G		not specified	Uncertain significance (Apr 28, 2023)
4-150224520-G-T		not specified	Uncertain significance (Sep 22, 2023)
4-150232339-A-G			Likely benign (Nov 01, 2023)
4-150232713-C-T		not specified	Uncertain significance (Dec 08, 2023)
4-150232764-A-G		not specified	Uncertain significance (Oct 12, 2021)
4-150232793-A-G		not specified	Uncertain significance (Dec 19, 2022)
4-150239752-A-T		not specified	Uncertain significance (Aug 19, 2023)
4-150247640-T-G		not specified	Uncertain significance (Aug 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DCLK2	protein_coding	protein_coding	ENST00000302176	17	179184

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.957	0.0429	125738	0	10	125748	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.76	334	437	0.764	0.0000231	5044
Missense in Polyphen		100	164.79	0.60683		1877
Synonymous	-0.308	180	175	1.03	0.00000987	1574
Loss of Function	4.66	6	36.3	0.165	0.00000199	433

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000353	0.0000352
Middle Eastern	0.0000544	0.0000544
South Asian	0.000132	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Protein kinase with a significantly reduced C(a2+)/CAM affinity and dependence compared to other members of the CaMK family. May play a role in the down-regulation of CRE-dependent gene activation probably by phosphorylation of the CREB coactivator CRTC2/TORC2 and the resulting retention of TORC2 in the cytoplasm (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.101

Intolerance Scores

• loftool: 0.182
• rvis_EVS: -0.38
• rvis_percentile_EVS: 28.01

Haploinsufficiency Scores

• pHI: 0.140
• hipred: Y
• hipred_score: 0.728
• ghis: 0.609

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.253

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dclk2
• 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: dclk2a
• Affected structure: whole organism
• Phenotype tag: abnormal
• Phenotype quality: morphology

Gene ontology

• Biological process: microtubule cytoskeleton organization;peptidyl-serine phosphorylation;hippocampus development;pyramidal neuron development;intracellular signal transduction;negative regulation of protein localization to nucleus
• Cellular component: cytoplasm;microtubule
• Molecular function: protein serine/threonine kinase activity;ATP binding