NCKAP5

protein-coding

NCK associated protein 5

Gene summary

Predicted to be involved in microtubule bundle formation and microtubule depolymerization. Predicted to be active in microtubule plus-end. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_207363.3

Inheritance

—

ClinVar variants

U:275B:44

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.32

Max pathogenic AF

—

Genomic locus

chr2:132,671,788-133,568,463

External References & Databases

Ensembl (ENSG00000176771)

Transcript & Mutation Effects

hg38 • Region Span ~896.7 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 NCKAP5 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 281

not providedTotal: 27

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_207363.3. 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			2 clinvar	5 clinvar	7 clinvar	14
missense			266 clinvar	27 clinvar	5 clinvar	298
nonsense			3 clinvar			3
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	275	32	12	319

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 29 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_207363.3	RefSeq	NP_997246.2	18	MANE Select
ENST00000409261.6	Ensembl	ENSP00000387128.1	18	MANE Select
NM_207481.4	RefSeq	NP_997364.3	16	Standard
ENST00000358991.4	Ensembl	ENSP00000351882.4	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

microtubule bundle formation
microtubule depolymerization
biological_process

Cellular Component

cellular_component
microtubule plus-end

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000409261
Coding exons: 18
Length: 896661
Individuals with no LoFs: 124598
Homozygous LoFs: 0
Heterozygous LoFs: 42
Defined: 124640
p: 0.000169

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.368	1038	1.01e+3	1.03	0.0000534	12400
Missense (PolyPhen)		285	296.67	0.96067		3958
Synonymous	-0.192	403	398	1.01	0.0000233	3803
Loss of Function	5.33	23	71.7	0.321	0.00000408	917

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00026	0.00026	rare
Latino/Admixed American	0.000088	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00022	0.00022	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00020	0.00019	rare
South Asian	0.00028	0.00026	rare
Other	0.00018	0.00017	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.994
RVIS EVS: 0.65
RVIS percentile EVS: 84.13

Essentials

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

Gene Damage Prediction

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