DCLK1

doublecortin like kinase 1, the group of Doublecortin superfamily

Basic information

Region (hg38): 13:35768651-36131382

Previous symbols: [ "DCAMKL1" ]

Links

ENSG00000133083 ∙ NCBI:9201 ∙ OMIM:604742 ∙ HGNC:2700 ∙ Uniprot:O15075 ∙ 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 DCLK1 gene.

• Inborn genetic diseases (6 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DCLK1 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			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	2

Variants in DCLK1

This is a list of pathogenic ClinVar variants found in the DCLK1 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-35788282-C-G		not specified	Uncertain significance (Aug 02, 2021)
13-35805763-A-G		not specified	Uncertain significance (Feb 17, 2024)
13-35808235-C-T			Uncertain significance (Sep 01, 2023)
13-35810836-C-T		not specified	Uncertain significance (Dec 09, 2023)
13-35822777-C-T			Benign (Aug 06, 2018)
13-35822821-C-T		not specified	Uncertain significance (Nov 09, 2022)
13-35822831-G-A			Benign (Jun 18, 2018)
13-35839143-C-T		not specified	Uncertain significance (Jan 26, 2022)
13-35854509-C-T		not specified	Uncertain significance (Nov 22, 2022)
13-35871254-G-A		not specified	Uncertain significance (May 11, 2022)
13-36112092-G-A		not specified	Uncertain significance (Dec 19, 2023)
13-36112132-C-T		not specified	Uncertain significance (Oct 03, 2023)
13-36126043-C-A		not specified	Uncertain significance (Feb 15, 2023)
13-36126073-C-A		not specified	Uncertain significance (Dec 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DCLK1	protein_coding	protein_coding	ENST00000255448	17	359966

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000363	125736	0	12	125748	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	4.40	177	436	0.406	0.0000259	4712
Missense in Polyphen		8	25.065	0.31917		217
Synonymous	1.59	153	180	0.849	0.0000121	1450
Loss of Function	5.30	4	40.4	0.0991	0.00000236	459

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000323	0.000323
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable kinase that may be involved in a calcium- signaling pathway controlling neuronal migration in the developing brain. May also participate in functions of the mature nervous system.

Recessive Scores

• pRec: 0.163

Intolerance Scores

• loftool: 0.427
• rvis_EVS: -0.65
• rvis_percentile_EVS: 16.44

Haploinsufficiency Scores

• pHI: 0.830
• hipred: Y
• hipred_score: 0.658
• ghis: 0.633

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.743

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dclk1
• Phenotype: cellular phenotype; homeostasis/metabolism phenotype; 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); digestive/alimentary 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); reproductive system phenotype; neoplasm

Gene ontology

• Biological process: neuron migration;protein phosphorylation;nervous system development;central nervous system development;response to virus;endosomal transport;peptidyl-serine phosphorylation;central nervous system projection neuron axonogenesis;forebrain development;intracellular signal transduction;axon extension;dendrite morphogenesis;negative regulation of protein localization to nucleus
• Cellular component: integral component of plasma membrane;postsynaptic density
• Molecular function: protein kinase activity;protein serine/threonine kinase activity;ATP binding