KNTC1
Basic information
Region (hg38): 12:122527246-122626396
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (194 variants)
- not_provided (3 variants)
- Prostate_cancer (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the KNTC1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000014708.6. 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 | 3 | |||||
| missense | 188 | 195 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 188 | 10 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| KNTC1 | protein_coding | protein_coding | ENST00000333479 | 63 | 99151 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 5.33e-43 | 0.779 | 124407 | 0 | 251 | 124658 | 0.00101 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.913 | 968 | 1.05e+3 | 0.921 | 0.0000526 | 14424 |
| Missense in Polyphen | 388 | 442.46 | 0.87692 | 6277 | ||
| Synonymous | 0.543 | 373 | 387 | 0.965 | 0.0000208 | 4016 |
| Loss of Function | 3.19 | 87 | 126 | 0.693 | 0.00000613 | 1720 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00251 | 0.00248 |
| Ashkenazi Jewish | 0.000298 | 0.000298 |
| East Asian | 0.00173 | 0.00167 |
| Finnish | 0.000345 | 0.000325 |
| European (Non-Finnish) | 0.00110 | 0.00106 |
| Middle Eastern | 0.00173 | 0.00167 |
| South Asian | 0.000899 | 0.000883 |
| Other | 0.000552 | 0.000495 |
dbNSFP
Source:
- Function
- FUNCTION: Essential component of the mitotic checkpoint, which prevents cells from prematurely exiting mitosis. Required for the assembly of the dynein-dynactin and MAD1-MAD2 complexes onto kinetochores (PubMed:11146660, PubMed:11590237, PubMed:15824131). Its function related to the spindle assembly machinery is proposed to depend on its association in the mitotic RZZ complex. {ECO:0000269|PubMed:11146660, ECO:0000269|PubMed:11590237, ECO:0000269|PubMed:15824131, ECO:0000305}.;
- Pathway
- Signal Transduction;Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal;Amplification of signal from the kinetochores;Mitotic Spindle Checkpoint;Cell Cycle Checkpoints;RHO GTPases Activate Formins;RHO GTPase Effectors;Signaling by Rho GTPases;Mitotic Prometaphase;Separation of Sister Chromatids;Mitotic Anaphase;Mitotic Metaphase and Anaphase;M Phase;Cell Cycle;Resolution of Sister Chromatid Cohesion;Cell Cycle, Mitotic
(Consensus)
Recessive Scores
- pRec
- 0.145
Intolerance Scores
- loftool
- 0.998
- rvis_EVS
- 0.49
- rvis_percentile_EVS
- 79.48
Haploinsufficiency Scores
- pHI
- 0.531
- hipred
- N
- hipred_score
- 0.319
- ghis
- 0.603
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.765
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Kntc1
- 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); pigmentation phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); limbs/digits/tail phenotype; vision/eye phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- mitotic cell cycle checkpoint;regulation of exit from mitosis;cell division;protein-containing complex assembly
- Cellular component
- condensed chromosome kinetochore;spindle pole;nucleus;kinetochore microtubule;cytosol;plasma membrane;actin cytoskeleton;RZZ complex
- Molecular function
- protein binding