CENPH
centromere protein H, the group of Constitutive centromere associated network
Basic information
Region (hg38): 5:69189574-69210357
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 CENPH 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 | 20 | 21 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 20 | 1 | 0 |
Variants in CENPH
This is a list of pathogenic ClinVar variants found in the CENPH region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 5-69189648-C-T | not specified | Uncertain significance (Feb 25, 2025) | ||
| 5-69189654-T-G | not specified | Uncertain significance (Jun 11, 2021) | ||
| 5-69189695-C-T | not specified | Uncertain significance (Jan 19, 2025) | ||
| 5-69189748-C-G | not specified | Uncertain significance (May 13, 2024) | ||
| 5-69189765-T-C | not specified | Uncertain significance (Aug 28, 2024) | ||
| 5-69191800-G-C | not specified | Uncertain significance (Dec 14, 2023) | ||
| 5-69191802-G-A | not specified | Uncertain significance (Nov 18, 2022) | ||
| 5-69191840-G-T | not specified | Uncertain significance (Jan 19, 2025) | ||
| 5-69194661-C-T | not specified | Uncertain significance (Feb 06, 2024) | ||
| 5-69194689-T-A | not specified | Uncertain significance (Feb 05, 2024) | ||
| 5-69195719-A-T | not specified | Uncertain significance (Oct 11, 2024) | ||
| 5-69195722-T-G | not specified | Uncertain significance (May 25, 2022) | ||
| 5-69202517-A-G | not specified | Uncertain significance (Aug 02, 2021) | ||
| 5-69202552-A-G | not specified | Uncertain significance (Jul 16, 2024) | ||
| 5-69202556-T-C | not specified | Uncertain significance (Oct 26, 2021) | ||
| 5-69202959-A-G | not specified | Uncertain significance (Mar 31, 2024) | ||
| 5-69202969-G-T | not specified | Uncertain significance (Sep 20, 2023) | ||
| 5-69208223-T-C | not specified | Uncertain significance (Jan 04, 2022) | ||
| 5-69208243-A-G | not specified | Uncertain significance (Oct 07, 2024) | ||
| 5-69208260-T-G | not specified | Uncertain significance (Feb 28, 2024) | ||
| 5-69208299-C-G | not specified | Uncertain significance (Sep 16, 2021) | ||
| 5-69208304-G-A | not specified | Likely benign (Jan 23, 2023) | ||
| 5-69208325-T-C | not specified | Uncertain significance (Jun 30, 2024) | ||
| 5-69208343-T-C | Recurrent spontaneous abortion | Uncertain significance (Jan 27, 2020) | ||
| 5-69209761-A-G | not specified | Uncertain significance (Mar 25, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CENPH | protein_coding | protein_coding | ENST00000283006 | 9 | 20810 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.55e-7 | 0.636 | 125707 | 0 | 37 | 125744 | 0.000147 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.645 | 96 | 116 | 0.831 | 0.00000517 | 1635 |
| Missense in Polyphen | 22 | 24.382 | 0.90229 | 427 | ||
| Synonymous | -0.260 | 41 | 38.9 | 1.05 | 0.00000178 | 399 |
| Loss of Function | 1.12 | 13 | 18.1 | 0.716 | 0.00000106 | 206 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000415 | 0.000403 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000468 | 0.0000462 |
| European (Non-Finnish) | 0.000212 | 0.000202 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.000153 | 0.000131 |
| Other | 0.000179 | 0.000163 |
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. The CENPA-NAC complex recruits the CENPA-CAD (nucleosome distal) complex and may be involved in incorporation of newly synthesized CENPA into centromeres. Required for chromosome congression and efficiently align the chromosomes on a metaphase plate. {ECO:0000269|PubMed:14536089, ECO:0000269|PubMed:16875666, ECO:0000269|PubMed:18007590}.;
- 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;Nucleosome assembly;RHO GTPase Effectors;Signaling by Rho GTPases;Chromosome Maintenance;Deposition of new CENPA-containing nucleosomes at the centromere;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
- 0.0931
Intolerance Scores
- loftool
- 0.561
- rvis_EVS
- 0.01
- rvis_percentile_EVS
- 54.95
Haploinsufficiency Scores
- pHI
- 0.173
- hipred
- Y
- hipred_score
- 0.565
- ghis
- 0.654
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.539
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cenph
- 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); vision/eye phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan);
Zebrafish Information Network
- Gene name
- cenph
- Affected structure
- trunk
- Phenotype tag
- abnormal
- Phenotype quality
- curved dorsal
Gene ontology
- Biological process
- CENP-A containing nucleosome assembly;kinetochore assembly;kinetochore organization
- Cellular component
- kinetochore;condensed chromosome kinetochore;nucleus;nucleoplasm;nucleolus;cytosol
- Molecular function
- protein binding;kinetochore binding