CKAP2

protein-coding

cytoskeleton associated protein 2

Gene summary

This gene encodes a cytoskeleton-associated protein that stabalizes microtubules and plays a role in the regulation of cell division. The encoded protein is itself regulated through phosphorylation at multiple serine and threonine residues. There is a pseudogene of this gene on chromosome 14. Alternative splicing results in multiple transcript variations. [provided by RefSeq, Nov 2013]

MANE transcript

NM_018204.5

Inheritance

—

ClinVar variants

U:88B:13

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.79

Max pathogenic AF

—

Genomic locus

chr13:52,455,429-52,476,628

External References & Databases

Ensembl (ENSG00000136108)

Transcript & Mutation Effects

hg38 • Region Span ~21.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CKAP2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 93

not providedTotal: 7

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018204.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar		1 clinvar	2
missense			85 clinvar	9 clinvar	3 clinvar	97
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	88	9	4	101

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 27 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018204.5	RefSeq	NP_060674.3	9	MANE Select
ENST00000258607.10	Ensembl	ENSP00000258607.5	9	MANE Select
NM_001098525.3	RefSeq	NP_001091995.1	9	Standard
NM_001286686.2	RefSeq	NP_001273615.1	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

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

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000378037
Coding exons: 9
Length: 21200
Individuals with no LoFs: 125719
Homozygous LoFs: 0
Heterozygous LoFs: 29
Defined: 125748
p: 0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.403	376	355	1.06	0.0000176	4499
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00041	0.00037	rare
Latino/Admixed American	0.000088	0.000087	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.000057	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00012	0.00011	rare
South Asian	0.00014	0.00013	rare
Other	0.00020	0.00016	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.117

Gene Damage Prediction

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