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

ENSG00000175216 ∙ NCBI:9793 ∙ OMIM:611142 ∙ HGNC:28959 ∙ Uniprot:Q14008 ∙ 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 CKAP5 gene.

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.

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				5		5
missense			66	1		67
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	66	6	0

Variants in CKAP5

This is a list of pathogenic ClinVar variants found in the CKAP5 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-46744099-A-C		not specified	Uncertain significance (Mar 22, 2023)
11-46744249-G-C		not specified	Uncertain significance (Jun 16, 2023)
11-46744548-C-T		not specified	Uncertain significance (Aug 10, 2023)
11-46750307-T-C		not specified	Uncertain significance (Mar 21, 2023)
11-46750325-G-A		not specified	Uncertain significance (Aug 21, 2023)
11-46750378-G-T		not specified	Uncertain significance (Feb 12, 2024)
11-46750536-T-G		not specified	Uncertain significance (Sep 07, 2022)
11-46751219-C-T		not specified	Uncertain significance (Dec 15, 2022)
11-46751220-G-A			Likely benign (Feb 01, 2023)
11-46751238-C-T			Likely benign (Apr 01, 2022)
11-46751430-C-G		not specified	Uncertain significance (Apr 07, 2023)
11-46751513-G-A			Likely benign (Feb 01, 2023)
11-46752657-T-C		not specified	Uncertain significance (May 14, 2024)
11-46752676-C-T		not specified	Uncertain significance (Dec 16, 2022)
11-46752683-G-T		not specified	Uncertain significance (Jan 29, 2024)
11-46753455-C-T		not specified	Uncertain significance (Mar 01, 2024)
11-46754924-G-C		not specified	Uncertain significance (Feb 15, 2023)
11-46755028-T-C		not specified	Uncertain significance (Sep 12, 2023)
11-46758940-T-C		not specified	Uncertain significance (Feb 26, 2024)
11-46759018-C-T		not specified	Uncertain significance (Oct 12, 2021)
11-46759038-C-T		not specified	Uncertain significance (Feb 27, 2023)
11-46759344-A-G		not specified	Uncertain significance (May 27, 2022)
11-46759434-C-A		not specified	Uncertain significance (May 11, 2022)
11-46760709-T-C		not specified	Uncertain significance (Jun 22, 2023)
11-46760712-T-C		not specified	Likely benign (Oct 03, 2022)

GnomAD

Source: gnomAD

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: dbNSFP

• 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