NEK5

protein-coding

NIMA related kinase 5

Gene summary

Predicted to enable protein kinase activity. Predicted to act upstream of or within positive regulation of striated muscle cell differentiation. Located in sperm flagellum. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001365552.1

Inheritance

—

ClinVar variants

U:94B:8

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.89

Max pathogenic AF

—

Genomic locus

chr13:52,033,611-52,129,092

External References & Databases

Ensembl (ENSG00000197168)

Transcript & Mutation Effects

hg38 • Region Span ~95.5 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 NEK5 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 103

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001365552.1. 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
missense			91 clinvar	7 clinvar		98
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	94	8	0	102

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 32 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001365552.1	RefSeq	NP_001352481.1	22	MANE Select
ENST00000684899.1	Ensembl	ENSP00000509632.1	22	MANE Select
NM_199289.3	RefSeq	NP_954983.1	20	Standard
ENST00000355568.8	Ensembl	ENSP00000347767.4	20	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

protein phosphorylation
positive regulation of striated muscle cell differentiation
positive regulation of cysteine-type endopeptidase activity

Molecular Function

protein serine/threonine kinase activity
ATP binding
metal ion binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000355568
Coding exons: 20
Length: 92122
Individuals with no LoFs: 125524
Homozygous LoFs: 2
Heterozygous LoFs: 222
Defined: 125748
p: 0.000891

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.423	346	369	0.938	0.0000184	4713
Missense (PolyPhen)		104	116.78	0.8906		1536
Synonymous	0.452	120	126	0.949	0.00000687	1236
Loss of Function	0.642	38	42.5	0.894	0.00000223	520

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0065	0.0064	notable
Latino/Admixed American	0.00088	0.00087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00038	0.00038	rare
Finnish	0.000092	0.000092	rare
European (Non-Finnish)	0.00048	0.00048	rare
South Asian	0.00080	0.00075	rare
Other	0.00065	0.00065	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.980
RVIS EVS: 1.07
RVIS percentile EVS: 91.67

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.396

Gene Damage Prediction

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