CHRAC1
Basic information
Region (hg38): 8:140511311-140517154
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 CHRAC1 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 | 3 | 1 | 0 |
Variants in CHRAC1
This is a list of pathogenic ClinVar variants found in the CHRAC1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 8-140511510-T-C | not specified | Uncertain significance (Mar 06, 2023) | ||
| 8-140511537-A-G | not specified | Uncertain significance (May 23, 2023) | ||
| 8-140514469-A-G | not specified | Uncertain significance (Jun 03, 2024) | ||
| 8-140515161-C-G | not specified | Uncertain significance (Dec 01, 2022) | ||
| 8-140515193-A-C | not specified | Likely benign (Dec 07, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CHRAC1 | protein_coding | protein_coding | ENST00000220913 | 3 | 5840 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0695 | 0.751 | 114742 | 0 | 2 | 114744 | 0.00000872 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.349 | 50 | 57.4 | 0.871 | 0.00000256 | 842 |
| Missense in Polyphen | 13 | 16.965 | 0.76627 | 253 | ||
| Synonymous | 0.479 | 20 | 22.9 | 0.873 | 0.00000110 | 233 |
| Loss of Function | 0.928 | 2 | 4.00 | 0.499 | 1.67e-7 | 63 |
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) | 0.00000936 | 0.00000925 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000395 | 0.0000376 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Forms a complex with DNA polymerase epsilon subunit POLE3 and binds naked DNA, which is then incorporated into chromatin, aided by the nucleosome remodeling activity of ISWI/SNF2H and ACF1.;
Recessive Scores
- pRec
- 0.114
Intolerance Scores
- loftool
- 0.561
- rvis_EVS
- 0.57
- rvis_percentile_EVS
- 81.89
Haploinsufficiency Scores
- pHI
- 0.153
- hipred
- Y
- hipred_score
- 0.705
- ghis
- 0.436
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.961
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Chrac1
- Phenotype
Zebrafish Information Network
- Gene name
- chrac1
- Affected structure
- primitive erythrocyte differentiation
- Phenotype tag
- abnormal
- Phenotype quality
- decreased occurrence
Gene ontology
- Biological process
- chromatin remodeling;heterochromatin organization involved in chromatin silencing;DNA biosynthetic process
- Cellular component
- epsilon DNA polymerase complex;CHRAC
- Molecular function
- DNA binding;DNA-directed DNA polymerase activity;protein binding;protein heterodimerization activity