GeneBe

NEK6

protein-coding

NIMA related kinase 6

Gene summary

The protein encoded by this gene is a kinase required for progression through the metaphase portion of mitosis. Inhibition of the encoded protein can lead to apoptosis. This protein also can enhance tumorigenesis by suppressing tumor cell senescence. Several transcript variants encoding a few different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]

MANE transcript

NM_014397.6

Inheritance

—

ClinVar variants

U:43B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.31

Max pathogenic AF

—

Genomic locus

chr9:124,257,606-124,353,307

External References & Databases

Ensembl (ENSG00000119408)NCBI Gene (10783)OMIM (604884)HGNC:7749GenCCUniProt (Q9HC98)AlphaFoldClinVar (NEK6)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~95.7 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 NEK6 variants in ClinVar

2 Conditions Cataloged
not specifiedTotal: 44
not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014397.6. 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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
1
clinvar
 2
missense
39
clinvar
3
clinvar
 42
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
3
clinvar
 3
Total00433147
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 60 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_014397.6RefSeqNP_055212.29MANE Select
ENST00000320246.10EnsemblENSP00000319734.59MANE Select
NM_001145001.3RefSeqNP_001138473.110Standard
NM_001166167.2RefSeqNP_001159639.110Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Nuclear Pore Complex (NPC) Disassembly
  • Activation of NIMA Kinases NEK9, NEK6, NEK7
  • Nuclear Envelope Breakdown
  • Mitotic Prophase
  • M Phase

Biological Process

  • protein phosphorylation
  • apoptotic process
  • chromosome segregation
  • mitotic nuclear envelope disassembly
  • regulation of mitotic cell cycle

Molecular Function

  • magnesium ion binding
  • transcription corepressor binding
  • protein serine/threonine kinase activity
  • protein binding
  • ATP binding

Cellular Component

  • spindle pole
  • nucleus
  • nucleoplasm
  • cytoplasm
  • centrosome

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000373600
Coding exons
10
Length
95702
Individuals with no LoFs
125730
Homozygous LoFs
0
Heterozygous LoFs
17
Defined
125747
p
0.0000676
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense1.951312110.6210.00001282271
Missense (PolyPhen)3376.0220.43408791
Synonymous0.3918690.70.9480.00000651631
Loss of Function2.82619.40.3090.00000101217

Population LoF Frequency

PopulationCAFp-valueStatus
African0.0000620.000062rare
Latino/Admixed American0.0000880.000087rare
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish00.0absent
European (Non-Finnish)0.0000880.000088rare
South Asian0.0000980.000098rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Protein kinase which plays an important role in mitotic cell cycle progression. Required for chromosome segregation at metaphase-anaphase transition, robust mitotic spindle formation and cytokinesis. Phosphorylates ATF4, CIR1, PTN, RAD26L, RBBP6, RPS7, RPS6KB1, TRIP4, STAT3 and histones H1 and H3. Phosphorylates KIF11 to promote mitotic spindle formation. Involved in G2/M phase cell cycle arrest induced by DNA damage. Inhibition of activity results in apoptosis. May contribute to tumorigenesis by suppressing p53/TP53-induced cancer cell senescence. {ECO:0000269|PubMed:12054534, ECO:0000269|PubMed:14563848, ECO:0000269|PubMed:18728393, ECO:0000269|PubMed:19001501, ECO:0000269|PubMed:19414596, ECO:0000269|PubMed:20407017, ECO:0000269|PubMed:20873783, ECO:0000269|PubMed:21099361}.;

Recessive Scores

pRec
0.114

Intolerance Scores

LoFtool
0.533
RVIS EVS
-0.36
RVIS percentile EVS
28.93

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.997

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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