DCLK1
Basic information
Region (hg38): 13:35768652-36131382
Previous symbols: [ "DCAMKL1" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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 | |||||
| missense | 12 | 12 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 12 | 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) | ||
| 13-35793401-G-A | not specified | Uncertain significance (May 16, 2024) | ||
| 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) | ||
| 13-36112077-C-T | not specified | Uncertain significance (May 26, 2024) | ||
| 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:
| 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:
- 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