CKAP2

cytoskeleton associated protein 2

Basic information

Region (hg38): 13:52455429-52476628

Links

ENSG00000136108 ∙ NCBI:26586 ∙ OMIM:611569 ∙ HGNC:1990 ∙ Uniprot:Q8WWK9 ∙ 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 CKAP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CKAP2 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					1	1
missense			50	7	3	60
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	50	7	5

Variants in CKAP2

This is a list of pathogenic ClinVar variants found in the CKAP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-52455576-C-T		not specified	Uncertain significance (Jun 04, 2024)
13-52455635-CGCGGTG-C			Benign (Apr 16, 2022)
13-52456571-T-C		not specified	Uncertain significance (Nov 08, 2021)
13-52460940-A-G		not specified	Uncertain significance (Aug 07, 2024)
13-52460948-A-G		not specified	Uncertain significance (Mar 23, 2022)
13-52460958-A-C		not specified	Uncertain significance (Apr 12, 2022)
13-52461124-A-G		not specified	Uncertain significance (Jan 23, 2025)
13-52461155-A-G			Benign (Jul 06, 2018)
13-52461163-G-C		not specified	Uncertain significance (Jan 26, 2022)
13-52461203-C-T		not specified	Uncertain significance (Feb 16, 2023)
13-52461206-C-T		not specified	Likely benign (May 24, 2024)
13-52461250-A-C		not specified	Uncertain significance (May 23, 2024)
13-52461343-C-T		not specified	Uncertain significance (Nov 13, 2023)
13-52461457-A-G		not specified	Likely benign (Jun 07, 2023)
13-52461460-C-T		not specified	Likely benign (Feb 27, 2024)
13-52461466-G-T		not specified	Uncertain significance (Aug 26, 2024)
13-52461514-A-G		not specified	Likely benign (Dec 02, 2024)
13-52461527-A-G		not specified	Uncertain significance (Mar 05, 2025)
13-52461541-A-C		not specified	Uncertain significance (Sep 27, 2021)
13-52461577-C-G		not specified	Uncertain significance (Jan 19, 2025)
13-52461604-C-T			Likely benign (Dec 31, 2019)
13-52461605-A-C		not specified	Uncertain significance (Nov 10, 2024)
13-52461605-A-T		not specified	Uncertain significance (Dec 09, 2024)
13-52461617-G-A		not specified	Likely benign (Oct 04, 2022)
13-52461628-A-C		not specified	Uncertain significance (Oct 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CKAP2	protein_coding	protein_coding	ENST00000378037	9	21200

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.18e-13	0.244	125719	0	29	125748	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.403	376	355	1.06	0.0000176	4499
Missense in Polyphen		57	60.718	0.93877		893
Synonymous	-0.439	134	128	1.05	0.00000626	1293
Loss of Function	1.04	22	27.9	0.788	0.00000148	364

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000496	0.000458
Ashkenazi Jewish	0.000100	0.0000992
East Asian	0.0000570	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000115	0.000114
Middle Eastern	0.0000570	0.0000544
South Asian	0.000137	0.000131
Other	0.000198	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Possesses microtubule stabilizing properties. Involved in regulating aneuploidy, cell cycling, and cell death in a p53/TP53-dependent manner (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.993

Intolerance Scores

• loftool: 0.970
• rvis_EVS: 1.22
• rvis_percentile_EVS: 93.24

Haploinsufficiency Scores

• pHI: 0.369
• hipred: N
• hipred_score: 0.486
• ghis: 0.567

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.117

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ckap2

Gene ontology

• Biological process: mitotic cytokinesis;apoptotic process;negative regulation of microtubule depolymerization;positive regulation of transcription by RNA polymerase II
• Cellular component: spindle pole;centrosome;cytosol;cytoplasmic microtubule;microtubule cytoskeleton