CKAP5
cytoskeleton associated protein 5, the group of MicroRNA protein coding host genes|Small nucleolar RNA protein coding host genes|TOG domain containing
Basic information
Region (hg38): 11:46743048-46846308
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (163 variants)
- not_provided (7 variants)
- Prostate_cancer (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CKAP5 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001008938.4. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 6 | |||||
| missense | 161 | 164 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 162 | 9 | 0 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CKAP5 | protein_coding | protein_coding | ENST00000529230 | 43 | 103250 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 2.30e-10 | 125719 | 0 | 28 | 125747 | 0.000111 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.78 | 722 | 1.07e+3 | 0.675 | 0.0000543 | 13388 |
| Missense in Polyphen | 165 | 317.49 | 0.5197 | 4144 | ||
| Synonymous | 1.79 | 335 | 379 | 0.883 | 0.0000190 | 3880 |
| Loss of Function | 8.59 | 10 | 105 | 0.0952 | 0.00000570 | 1296 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000151 | 0.000151 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000109 | 0.000109 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.000142 | 0.000132 |
| Middle Eastern | 0.000109 | 0.000109 |
| South Asian | 0.000132 | 0.000131 |
| Other | 0.000336 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: Binds to the plus end of microtubules and regulates microtubule dynamics and microtubule organization. Acts as processive microtubule polymerase. Promotes cytoplasmic microtubule nucleation and elongation. Plays a major role in organizing spindle poles. In spindle formation protects kinetochore microtubules from depolymerization by KIF2C and has an essential role in centrosomal microtubule assembly independently of KIF2C activity. Contributes to centrosome integrity. Acts as component of the TACC3/ch-TOG/clathrin complex proposed to contribute to stabilization of kinetochore fibers of the mitotic spindle by acting as inter-microtubule bridge. The TACC3/ch- TOG/clathrin complex is required for the maintenance of kinetochore fiber tension (PubMed:23532825). Enhances the strength of NDC80 complex-mediated kinetochore-tip microtubule attachments (PubMed:27156448). {ECO:0000269|PubMed:12569123, ECO:0000269|PubMed:18809577, ECO:0000269|PubMed:21297582, ECO:0000269|PubMed:21646404, ECO:0000269|PubMed:23532825, ECO:0000269|PubMed:27156448, ECO:0000269|PubMed:9570755}.;
- Pathway
- Signal Transduction;Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal;Amplification of signal from the kinetochores;Mitotic Spindle Checkpoint;Cell Cycle Checkpoints;RHO GTPases Activate Formins;Aurora A signaling;RHO GTPase Effectors;Signaling by Rho GTPases;Regulation of PLK1 Activity at G2/M Transition;Recruitment of mitotic centrosome proteins and complexes;Loss of Nlp from mitotic centrosomes;Loss of proteins required for interphase microtubule organization from the centrosome;Centrosome maturation;AURKA Activation by TPX2;G2/M Transition;Mitotic G2-G2/M phases;Recruitment of NuMA to mitotic centrosomes;Mitotic Prometaphase;Separation of Sister Chromatids;Mitotic Anaphase;Mitotic Metaphase and Anaphase;M Phase;Cell Cycle;Resolution of Sister Chromatid Cohesion;Integrin-linked kinase signaling;Cell Cycle, Mitotic;Anchoring of the basal body to the plasma membrane;Cilium Assembly;Organelle biogenesis and maintenance
(Consensus)
Recessive Scores
- pRec
- 0.188
Intolerance Scores
- loftool
- 0.349
- rvis_EVS
- -1.61
- rvis_percentile_EVS
- 2.98
Haploinsufficiency Scores
- pHI
- 0.849
- hipred
- Y
- hipred_score
- 0.758
- ghis
- 0.676
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.850
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ckap5
- Phenotype
- growth/size/body region phenotype; digestive/alimentary phenotype; craniofacial 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);
Gene ontology
- Biological process
- G2/M transition of mitotic cell cycle;microtubule depolymerization;spindle organization;centrosome cycle;regulation of G2/M transition of mitotic cell cycle;establishment or maintenance of microtubule cytoskeleton polarity;microtubule polymerization;RNA transport;centrosome duplication;cell division;ciliary basal body-plasma membrane docking
- Cellular component
- kinetochore;condensed chromosome kinetochore;spindle pole;gamma-tubulin complex;nucleolus;centrosome;cytosol;plasma membrane;microtubule cytoskeleton;membrane;protein-containing complex;microtubule plus-end
- Molecular function
- protein binding;cadherin binding;microtubule plus-end binding