NEK6

NIMA related kinase 6

Basic information

Region (hg38): 9:124257606-124353307

Links

ENSG00000119408 ∙ NCBI:10783 ∙ OMIM:604884 ∙ HGNC:7749 ∙ Uniprot:Q9HC98 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NEK6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NEK6 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			20	2		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	21	2	1

Variants in NEK6

This is a list of pathogenic ClinVar variants found in the NEK6 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
9-124292962-T-A		not specified	Uncertain significance (Oct 12, 2021)
9-124292965-G-A		not specified	Uncertain significance (May 20, 2024)
9-124293011-G-A		not specified	Uncertain significance (May 18, 2023)
9-124293011-G-T		not specified	Uncertain significance (Jun 03, 2022)
9-124301939-G-A		not specified	Uncertain significance (Jun 06, 2023)
9-124301993-A-G		not specified	Uncertain significance (Nov 10, 2022)
9-124302001-A-T		not specified	Uncertain significance (Oct 22, 2021)
9-124302004-T-C		not specified	Likely benign (Oct 22, 2021)
9-124302012-C-A		not specified	Uncertain significance (Mar 29, 2022)
9-124302028-G-T		not specified	Uncertain significance (Mar 21, 2023)
9-124312521-A-G		not specified	Likely benign (Jan 17, 2024)
9-124312522-C-T		not specified	Uncertain significance (Nov 19, 2022)
9-124312560-G-A		not specified	Uncertain significance (Nov 30, 2021)
9-124312590-G-A		not specified	Uncertain significance (Jun 03, 2024)
9-124313961-T-C			Benign (Jul 23, 2018)
9-124313973-C-G		not specified	Uncertain significance (Jan 03, 2024)
9-124321566-C-G		not specified	Uncertain significance (Jun 06, 2023)
9-124326358-C-T		not specified	Uncertain significance (Jul 26, 2022)
9-124326402-G-A		not specified	Uncertain significance (Oct 04, 2022)
9-124326420-C-T		not specified	Uncertain significance (Nov 07, 2022)
9-124339642-T-G		not specified	Uncertain significance (Jun 27, 2023)
9-124347747-G-A		not specified	Uncertain significance (Sep 23, 2023)
9-124347802-G-A		not specified	Uncertain significance (Jun 01, 2023)
9-124347817-G-A		not specified	Uncertain significance (Nov 12, 2021)
9-124350900-G-A		not specified	Uncertain significance (Oct 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NEK6	protein_coding	protein_coding	ENST00000373600	10	95702

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0389	0.960	125730	0	17	125747	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.95	131	211	0.621	0.0000128	2271
Missense in Polyphen		33	76.022	0.43408		791
Synonymous	0.391	86	90.7	0.948	0.00000651	631
Loss of Function	2.82	6	19.4	0.309	0.00000101	217

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000150	0.000150
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000883	0.0000879
Middle Eastern	0.00	0.00
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

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}.
• Pathway: Nuclear Pore Complex (NPC) Disassembly;Activation of NIMA Kinases NEK9, NEK6, NEK7;Nuclear Envelope Breakdown;Mitotic Prophase;M Phase;Cell Cycle;Cell Cycle, Mitotic (Consensus)

Recessive Scores

• pRec: 0.114

Intolerance Scores

• loftool: 0.533
• rvis_EVS: -0.36
• rvis_percentile_EVS: 28.93

Haploinsufficiency Scores

• pHI: 0.123
• hipred: Y
• hipred_score: 0.749
• ghis: 0.608

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.997

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nek6
• Phenotype: homeostasis/metabolism phenotype; muscle phenotype; normal phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); respiratory system phenotype

Gene ontology

• Biological process: protein phosphorylation;apoptotic process;chromosome segregation;mitotic nuclear envelope disassembly;regulation of mitotic cell cycle;peptidyl-serine phosphorylation;regulation of mitotic metaphase/anaphase transition;positive regulation of I-kappaB kinase/NF-kappaB signaling;protein autophosphorylation;spindle assembly;cell division;regulation of cellular senescence
• Cellular component: spindle pole;nucleus;nucleoplasm;cytoplasm;centrosome;microtubule organizing center;cytosol;microtubule;nuclear speck;protein-containing complex;intracellular membrane-bounded organelle
• Molecular function: magnesium ion binding;transcription corepressor binding;protein serine/threonine kinase activity;protein binding;ATP binding;kinesin binding;protein kinase binding;ubiquitin protein ligase binding;activating transcription factor binding