NEK11

protein-coding

NIMA related kinase 11

Gene summary

This gene encodes a member of the never in mitosis gene A family of kinases. The encoded protein localizes to the nucleoli, and may function with NEK2A in the S-phase checkpoint. The encoded protein appears to play roles in DNA replication and response to genotoxic stress. Alternatively spliced transcript variants have been described.[provided by RefSeq, Mar 2009]

MANE transcript

NM_024800.5

Inheritance

—

ClinVar variants

U:100B:12

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.92

Max pathogenic AF

—

Genomic locus

chr3:131,026,850-131,350,465

External References & Databases

Ensembl (ENSG00000114670)

Transcript & Mutation Effects

hg38 • Region Span ~323.6 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 NEK11 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 91

not providedTotal: 8

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024800.5. 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	8 clinvar		9
missense			92 clinvar	3 clinvar	1 clinvar	96
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	100	11	1	112

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 121 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024800.5	RefSeq	NP_079076.3	16	MANE Select
ENST00000383366.9	Ensembl	ENSP00000372857.4	16	MANE Select
NM_001146003.2	RefSeq	NP_001139475.1	15	Standard
NM_001321220.2	RefSeq	NP_001308149.1	16	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

protein phosphorylation
histone phosphorylation
intra-S DNA damage checkpoint
intracellular signal transduction
mitotic cell cycle phase transition

Molecular Function

protein serine/threonine kinase activity
protein binding
ATP binding
metal ion binding

Cellular Component

nucleoplasm
nucleolus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000383366
Coding exons: 16
Length: 323616
Individuals with no LoFs: 125562
Homozygous LoFs: 0
Heterozygous LoFs: 186
Defined: 125748
p: 0.000740

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.280	353	339	1.04	0.0000168	4259
Missense (PolyPhen)		110	99.309	1.1077		1305
Synonymous	0.526	113	120	0.939	0.00000648	1152
Loss of Function	0.455	34	37.0	0.919	0.00000191	465

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0014	0.0014	notable
Latino/Admixed American	0.00026	0.00026	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00027	0.00027	rare
Finnish	0.00097	0.00097	rare
European (Non-Finnish)	0.0010	0.00098	rare
South Asian	0.00043	0.00042	rare
Other	0.00065	0.00065	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Protein kinase which plays an important role in the G2/M checkpoint response to DNA damage. Controls degradation of CDC25A by directly phosphorylating it on residues whose phosphorylation is required for BTRC-mediated polyubiquitination and degradation. {ECO:0000269|PubMed:12154088, ECO:0000269|PubMed:19734889, ECO:0000269|PubMed:20090422}.;

Recessive Scores

pRec: 0.0904

Intolerance Scores

LoFtool: 0.983
RVIS EVS: 0.47
RVIS percentile EVS: 78.83

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.458

Gene Damage Prediction

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