NEK6
Basic information
Region (hg38): 9:124257606-124353307
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (41 variants)
- not_provided (1 variants)
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. These statistics are base on transcript: NM_000014397.6. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | |||||
| missense | 32 | 34 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 32 | 2 | 1 |
GnomAD
Source:
| 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:
- 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