CBX1
Basic information
Region (hg38): 17:48070052-48101478
Links
Phenotypes
GenCC
Source:
- neurodevelopmental disorder (Moderate), mode of inheritance: AD
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (9 variants)
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. These statistics are base on transcript: NM_001127228.2. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 9 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 9 | 0 | 0 |
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