NEK7
NIMA related kinase 7
Basic information
Region (hg38): 1:198156993-198322420
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the NEK7 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 | 0 | |||||
| missense | 11 | 11 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 11 | 0 | 0 |
Variants in NEK7
This is a list of pathogenic ClinVar variants found in the NEK7 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-198232599-G-C | not specified | Uncertain significance (Dec 02, 2021) | ||
| 1-198232636-A-G | not specified | Uncertain significance (Mar 20, 2023) | ||
| 1-198253043-G-T | not specified | Uncertain significance (Aug 08, 2023) | ||
| 1-198253106-C-T | not specified | Uncertain significance (Mar 30, 2024) | ||
| 1-198253119-G-A | not specified | Uncertain significance (Jan 07, 2022) | ||
| 1-198253175-G-A | not specified | Uncertain significance (Aug 04, 2023) | ||
| 1-198264132-A-G | not specified | Uncertain significance (Mar 15, 2024) | ||
| 1-198264185-A-C | not specified | Uncertain significance (Dec 14, 2023) | ||
| 1-198278016-T-C | not specified | Uncertain significance (Sep 12, 2023) | ||
| 1-198278027-A-G | not specified | Uncertain significance (Jan 30, 2024) | ||
| 1-198278060-A-T | not specified | Uncertain significance (Feb 13, 2024) | ||
| 1-198297228-C-G | not specified | Uncertain significance (Dec 28, 2023) | ||
| 1-198319464-A-G | not specified | Uncertain significance (Aug 02, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| NEK7 | protein_coding | protein_coding | ENST00000367385 | 9 | 165458 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.880 | 0.120 | 125680 | 0 | 12 | 125692 | 0.0000477 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.29 | 83 | 166 | 0.499 | 0.00000838 | 1986 |
| Missense in Polyphen | 15 | 53.426 | 0.28076 | 635 | ||
| Synonymous | -0.247 | 59 | 56.6 | 1.04 | 0.00000297 | 553 |
| Loss of Function | 3.54 | 3 | 20.1 | 0.149 | 0.00000116 | 229 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000290 | 0.0000290 |
| Ashkenazi Jewish | 0.000100 | 0.0000992 |
| East Asian | 0.0000546 | 0.0000544 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.0000534 | 0.0000528 |
| Middle Eastern | 0.0000546 | 0.0000544 |
| South Asian | 0.0000674 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Protein kinase which plays an important role in mitotic cell cycle progression. Required for microtubule nucleation activity of the centrosome, robust mitotic spindle formation and cytokinesis. Phosphorylates RPS6KB1. {ECO:0000269|PubMed:17101132, ECO:0000269|PubMed:17586473, ECO:0000269|PubMed:19414596}.;
- Pathway
- NOD-like receptor signaling pathway - Homo sapiens (human);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
- 0.112
Intolerance Scores
- loftool
- 0.532
- rvis_EVS
- -0.03
- rvis_percentile_EVS
- 51.4
Haploinsufficiency Scores
- pHI
- 0.249
- hipred
- Y
- hipred_score
- 0.749
- ghis
- 0.572
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.989
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Nek7
- Phenotype
- cellular phenotype; growth/size/body region phenotype; immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype;
Gene ontology
- Biological process
- protein phosphorylation;regulation of mitotic cell cycle;positive regulation of telomere maintenance via telomerase;spindle assembly;positive regulation of telomerase activity;positive regulation of telomere capping
- Cellular component
- spindle pole;nucleoplasm;cytoplasm;microtubule organizing center;microtubule
- Molecular function
- protein serine/threonine kinase activity;ATP binding;metal ion binding