CBX5
chromobox 5, the group of Chromobox family|MicroRNA protein coding host genes
Basic information
Region (hg38): 12:54230942-54280133
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 CBX5 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 | 0 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 0 | 0 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CBX5 | protein_coding | protein_coding | ENST00000209875 | 4 | 49163 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.932 | 0.0680 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.53 | 30 | 102 | 0.295 | 0.00000512 | 1277 |
| Missense in Polyphen | 8 | 51.806 | 0.15442 | 634 | ||
| Synonymous | 0.320 | 34 | 36.5 | 0.933 | 0.00000189 | 324 |
| Loss of Function | 2.71 | 0 | 8.55 | 0.00 | 3.57e-7 | 121 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Component of heterochromatin that recognizes and binds histone H3 tails methylated at 'Lys-9' (H3K9me), leading to epigenetic repression. In contrast, it is excluded from chromatin when 'Tyr-41' of histone H3 is phosphorylated (H3Y41ph). Can interact with lamin-B receptor (LBR). This interaction can contribute to the association of the heterochromatin with the inner nuclear membrane. Involved in the formation of functional kinetochore through interaction with MIS12 complex proteins. {ECO:0000269|PubMed:19783980}.;
- Pathway
- Gene expression (Transcription);Transcriptional Regulation by E2F6;Generic Transcription Pathway;Factors involved in megakaryocyte development and platelet production;SUMOylation of chromatin organization proteins;Post-translational protein modification;SUMO E3 ligases SUMOylate target proteins;Metabolism of proteins;RNA Polymerase II Transcription;SUMOylation;Hemostasis;Aurora B signaling;E2F transcription factor network
(Consensus)
Recessive Scores
- pRec
- 0.413
Intolerance Scores
- loftool
- rvis_EVS
- 0.04
- rvis_percentile_EVS
- 56.25
Haploinsufficiency Scores
- pHI
- 0.786
- hipred
- Y
- hipred_score
- 0.831
- ghis
- 0.706
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- K
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.994
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Low | Low | Low |
| Primary Immunodeficiency | Low | Low | Low |
| Cancer | Low | Low | Low |
Mouse Genome Informatics
- Gene name
- Cbx5
- Phenotype
- growth/size/body region 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); normal phenotype; hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype; immune system phenotype;
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;cellular response to DNA damage stimulus;blood coagulation;viral process;negative regulation of transcription, DNA-templated;negative regulation of G0 to G1 transition
- Cellular component
- histone deacetylase complex;kinetochore;nuclear chromosome, telomeric region;nucleus;nuclear envelope;nucleoplasm;nuclear heterochromatin;pericentric heterochromatin;nucleolus;chromocenter;PML body;transcriptional repressor complex;nuclear pericentric heterochromatin;protein-containing complex;histone methyltransferase complex;site of DNA damage;ribonucleoprotein complex
- Molecular function
- chromatin binding;protein binding;protein binding, bridging;methylated histone binding;identical protein binding;protein homodimerization activity;histone deacetylase binding;ribonucleoprotein complex binding;protein-containing complex binding;repressing transcription factor binding