CENPW
Basic information
Region (hg38): 6:126340115-126348875
Previous symbols: [ "C6orf173" ]
Links
Phenotypes
GenCC
Source:
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 CENPW 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 | 3 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 3 | 0 | 0 |
Variants in CENPW
This is a list of pathogenic ClinVar variants found in the CENPW region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 6-126340365-C-G | not specified | Uncertain significance (Jun 10, 2024) | ||
| 6-126340365-C-T | not specified | Uncertain significance (Jun 05, 2023) | ||
| 6-126340389-G-T | not specified | Uncertain significance (Sep 25, 2024) | ||
| 6-126346253-A-G | not specified | Uncertain significance (Feb 10, 2023) | ||
| 6-126346260-A-T | not specified | Uncertain significance (Jun 16, 2024) | ||
| 6-126346299-A-G | not specified | Uncertain significance (Jan 30, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CENPW | protein_coding | protein_coding | ENST00000368328 | 3 | 8702 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.405 | 0.560 | 125739 | 0 | 6 | 125745 | 0.0000239 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.749 | 33 | 47.5 | 0.694 | 0.00000227 | 556 |
| Missense in Polyphen | 13 | 14.226 | 0.9138 | 185 | ||
| Synonymous | 0.541 | 17 | 20.1 | 0.846 | 0.00000111 | 179 |
| Loss of Function | 1.68 | 1 | 5.09 | 0.196 | 2.79e-7 | 56 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000124 | 0.000123 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000353 | 0.0000352 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Component of the CENPA-NAC (nucleosome-associated) complex, a complex that plays a central role in assembly of kinetochore proteins, mitotic progression and chromosome segregation (By similarity). The CENPA-NAC complex recruits the CENPA-CAD (nucleosome distal) complex and may be involved in incorporation of newly synthesized CENPA into centromeres (By similarity). Part of a nucleosome-associated complex that binds specifically to histone H3-containing nucleosomes at the centromere, as opposed to nucleosomes containing CENPA. Component of the heterotetrameric CENP-T-W-S-X complex that binds and supercoils DNA, and plays an important role in kinetochore assembly. CENPW has a fundamental role in kinetochore assembly and function. It is one of the inner kinetochore proteins, with most further proteins binding downstream. Required for normal chromosome organization and normal progress through mitosis. {ECO:0000250, ECO:0000269|PubMed:19070575, ECO:0000269|PubMed:19533040, ECO:0000269|PubMed:21695110, ECO:0000269|PubMed:22002061, ECO:0000269|PubMed:22304917}.;
- Pathway
- Nucleosome assembly;Chromosome Maintenance;Deposition of new CENPA-containing nucleosomes at the centromere;Cell Cycle
(Consensus)
Recessive Scores
- pRec
- 0.0914
Intolerance Scores
- loftool
- rvis_EVS
- 0.5
- rvis_percentile_EVS
- 79.79
Haploinsufficiency Scores
- pHI
- 0.0783
- hipred
- N
- hipred_score
- 0.230
- ghis
- 0.424
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.231
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cenpw
- Phenotype
Zebrafish Information Network
- Gene name
- cenpw
- Affected structure
- Rohon-Beard neuron
- Phenotype tag
- abnormal
- Phenotype quality
- decreased branchiness
Gene ontology
- Biological process
- mitotic cell cycle;chromosome segregation;CENP-A containing nucleosome assembly;spindle assembly;chromosome organization;cell division;kinetochore assembly
- Cellular component
- chromosome, centromeric region;kinetochore;condensed chromosome kinetochore;nucleoplasm;nucleolus;nuclear matrix
- Molecular function
- DNA binding;protein binding;protein heterodimerization activity