CBX3
chromobox 3, the group of Chromobox family
Basic information
Region (hg38): 7:26201162-26213607
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 CBX3 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 | 2 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 2 | 0 | 0 |
Variants in CBX3
This is a list of pathogenic ClinVar variants found in the CBX3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 7-26206407-G-A | not specified | Uncertain significance (May 23, 2024) | ||
| 7-26206416-G-A | not specified | Uncertain significance (Jun 22, 2024) | ||
| 7-26206456-G-A | not specified | Uncertain significance (Jan 03, 2024) | ||
| 7-26208558-A-G | Recurrent spontaneous abortion | Uncertain significance (Jan 27, 2020) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CBX3 | protein_coding | protein_coding | ENST00000337620 | 5 | 12195 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.410 | 0.583 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.93 | 37 | 87.9 | 0.421 | 0.00000403 | 1198 |
| Missense in Polyphen | 6 | 18.464 | 0.32496 | 306 | ||
| Synonymous | -1.52 | 40 | 29.5 | 1.36 | 0.00000149 | 301 |
| Loss of Function | 2.24 | 2 | 9.43 | 0.212 | 4.58e-7 | 131 |
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: Seems to be involved in transcriptional silencing in heterochromatin-like complexes. Recognizes and binds histone H3 tails methylated at 'Lys-9', leading to epigenetic repression. May contribute to the association of the heterochromatin with the inner nuclear membrane through its interaction with lamin B receptor (LBR). Involved in the formation of functional kinetochore through interaction with MIS12 complex proteins. Contributes to the conversion of local chromatin to a heterochromatin-like repressive state through H3 'Lys-9' trimethylation, mediates the recruitment of the methyltransferases SUV39H1 and/or SUV39H2 by the PER complex to the E-box elements of the circadian target genes such as PER2 itself or PER1. Mediates the recruitement of NIPBL to sites of DNA damage at double-strand breaks (DSBs) (PubMed:28167679). {ECO:0000250|UniProtKB:P23198, ECO:0000269|PubMed:28167679}.;
- Pathway
- Exercise-induced Circadian Regulation;ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression;Positive epigenetic regulation of rRNA expression;Epigenetic regulation of gene expression;Gene expression (Transcription);Transcriptional Regulation by E2F6;Generic Transcription Pathway;RNA Polymerase II Transcription;RNA Polymerase I Transcription;RNA Polymerase I Chain Elongation
(Consensus)
Recessive Scores
- pRec
- 0.207
Intolerance Scores
- loftool
- 0.337
- rvis_EVS
- 0.06
- rvis_percentile_EVS
- 58
Haploinsufficiency Scores
- pHI
- 0.659
- hipred
- Y
- hipred_score
- 0.712
- ghis
- 0.523
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.965
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cbx3
- Phenotype
- endocrine/exocrine gland phenotype; 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);
Gene ontology
- Biological process
- chromatin remodeling;cellular response to DNA damage stimulus;negative regulation of transcription, DNA-templated;rhythmic process;negative regulation of G0 to G1 transition
- Cellular component
- chromosome, centromeric region;condensed chromosome, centromeric region;nuclear chromosome, telomeric region;chromatin;nucleus;nuclear envelope;nuclear inner membrane;nucleoplasm;nuclear euchromatin;nuclear heterochromatin;spindle;nuclear pericentric heterochromatin;site of DNA damage
- Molecular function
- protein binding;enzyme binding;protein domain specific binding;identical protein binding;histone methyltransferase binding