CBX1
Basic information
Region (hg38): 17:48070052-48101478
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 CBX1 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 | 4 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 4 | 0 | 0 |
Variants in CBX1
This is a list of pathogenic ClinVar variants found in the CBX1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 17-48071462-A-C | not specified | Uncertain significance (Mar 24, 2023) | ||
| 17-48071469-G-A | not specified | Uncertain significance (Feb 27, 2024) | ||
| 17-48076041-T-A | not specified | Uncertain significance (Aug 16, 2022) | ||
| 17-48076065-C-T | not specified | Uncertain significance (May 18, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CBX1 | protein_coding | protein_coding | ENST00000393408 | 4 | 31470 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.976 | 0.0238 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.54 | 28 | 99.3 | 0.282 | 0.00000532 | 1219 |
| Missense in Polyphen | 5 | 41.762 | 0.11973 | 506 | ||
| Synonymous | 0.907 | 30 | 37.0 | 0.810 | 0.00000202 | 325 |
| Loss of Function | 3.14 | 0 | 11.5 | 0.00 | 7.17e-7 | 128 |
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. Recognizes and binds histone H3 tails methylated at 'Lys-9', leading to epigenetic repression. Interaction with lamin B receptor (LBR) can contribute to the association of the heterochromatin with the inner nuclear membrane. {ECO:0000250|UniProtKB:P83917}.;
Intolerance Scores
- loftool
- 0.169
- rvis_EVS
- 0.06
- rvis_percentile_EVS
- 58
Haploinsufficiency Scores
- pHI
- 0.185
- hipred
- Y
- hipred_score
- 0.825
- ghis
- 0.622
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.961
Mouse Genome Informatics
- Gene name
- Cbx1
- Phenotype
- normal 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
- cellular response to DNA damage stimulus;negative regulation of transcription, DNA-templated
- Cellular component
- chromosome, centromeric region;nuclear chromosome, telomeric region;chromatin;female pronucleus;male pronucleus;nucleus;nucleoplasm;nuclear heterochromatin;pericentric heterochromatin;spindle;chromocenter;site of DNA damage
- Molecular function
- chromatin binding;protein binding;enzyme binding;protein homodimerization activity;histone methyltransferase binding