NCKAP5L

protein-coding

NCK associated protein 5 like

Gene summary

Involved in microtubule bundle formation and microtubule depolymerization. Located in centrosome and microtubule plus-end. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

KIAA1602

MANE transcript

NM_001037806.4

Inheritance

—

ClinVar variants

U:240B:14

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.21

Max pathogenic AF

—

Genomic locus

chr12:49,791,146-49,828,750

External References & Databases

Ensembl (ENSG00000167566)

Transcript & Mutation Effects

hg38 • Region Span ~37.6 kb

Loading mutation effect viewer...

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 NCKAP5L variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 237

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001037806.4. 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			3 clinvar	1 clinvar	2 clinvar	6
missense			233 clinvar	10 clinvar	1 clinvar	244
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	240	11	3	254

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 23 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001037806.4	RefSeq	NP_001032895.2	11	MANE Select
ENST00000335999.7	Ensembl	ENSP00000337998.6	11	MANE Select
NM_001368048.1	RefSeq	NP_001354977.1	11	Standard
ENST00000433948.5	Ensembl	ENSP00000402619.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

microtubule bundle formation
microtubule depolymerization

Molecular Function

protein binding

Cellular Component

cytoplasm
centrosome
microtubule plus-end

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000335999
Coding exons: 11
Length: 37605
Individuals with no LoFs: 124797
Homozygous LoFs: 0
Heterozygous LoFs: 30
Defined: 124827
p: 0.000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.741	656	712	0.922	0.0000424	8212
Missense (PolyPhen)		227	264.24	0.85905		3192
Synonymous	0.167	307	311	0.988	0.0000187	3001
Loss of Function	4.78	9	42.7	0.211	0.00000248	485

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000067	0.000064	rare
Latino/Admixed American	0.000097	0.000087	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00034	0.00022	rare
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.00016	0.00015	rare
South Asian	0.00011	0.000098	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Regulates microtubule organization and stabilization. Promotes microtubule growth and bundling formation and stabilizes microtubules by increasing intense acetylation of microtubules (PubMed:26482847, PubMed:26485573). Both tubulin-binding and homodimer formation are required for NCKAP5L-mediated microtubule bundle formation (PubMed:26485573). {ECO:0000269|PubMed:26482847, ECO:0000269|PubMed:26485573}.;

Intolerance Scores

LoFtool: 0.609
RVIS EVS: -0.79
RVIS percentile EVS: 12.62

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.539

Gene Damage Prediction

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