CHRAC1
protein-codingchromatin accessibility complex subunit 1, the group of Chromatin accessibility complex
Gene summary
CHRAC1 is a histone-fold protein that interacts with other histone-fold proteins to bind DNA in a sequence-independent manner. These histone-fold protein dimers combine within larger enzymatic complexes for DNA transcription, replication, and packaging.[supplied by OMIM, Apr 2004]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~5.8 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to CHRAC1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_017444.6. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 16 | 1 | 17 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 19 | 1 | 0 | 20 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_059140.1 | 3 | MANE Select | |
| Ensembl | ENSP00000220913.5 | 3 | MANE Select | |
| Ensembl | ENSP00000430484.1 | 2 | Standard | |
| Ensembl | ENSP00000428697.1 | 2 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| chrac1 | Danio rerio | Structure: primitive erythrocyte differentiation Quality: decreased occurrence abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- chromatin remodeling
- heterochromatin organization involved in chromatin silencing
- DNA biosynthetic process
Molecular Function
- DNA binding
- DNA-directed DNA polymerase activity
- protein binding
- protein heterodimerization activity
Cellular Component
- epsilon DNA polymerase complex
- CHRAC
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000220913
- Coding exons
- 3
- Length
- 5840
- Individuals with no LoFs
- 114742
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 2
- Defined
- 114744
- p
- 0.00000872
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.349 | 50 | 57.4 | 0.871 | 0.00000256 | 842 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.0000094 | 0.0000092 | rare |
| South Asian | 0.000040 | 0.000038 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
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
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.961
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |