CHAF1B
Basic information
Region (hg38): 21:36385392-36419015
Links
Phenotypes
GenCC
Source:
- intellectual disability (Limited), mode of inheritance: AR
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (54 variants)
- not_provided (7 variants)
- Prostate_cancer (1 variants)
- Attention_deficit_hyperactivity_disorder (1 variants)
- Global_developmental_delay (1 variants)
- Intellectual_disability (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHAF1B gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005441.3. 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 | 3 | |||||
| missense | 52 | 60 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 1 | 52 | 6 | 4 |
Highest pathogenic variant AF is 0.0000032225796
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CHAF1B | protein_coding | protein_coding | ENST00000314103 | 13 | 33638 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.428 | 0.572 | 125738 | 0 | 10 | 125748 | 0.0000398 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.82 | 240 | 333 | 0.720 | 0.0000191 | 3634 |
| Missense in Polyphen | 48 | 109.18 | 0.43966 | 1181 | ||
| Synonymous | 0.439 | 129 | 136 | 0.952 | 0.00000896 | 1120 |
| Loss of Function | 3.77 | 6 | 27.2 | 0.220 | 0.00000131 | 321 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000125 | 0.000124 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000573 | 0.0000544 |
| Finnish | 0.0000925 | 0.0000924 |
| European (Non-Finnish) | 0.0000265 | 0.0000264 |
| Middle Eastern | 0.0000573 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.000173 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Complex that is thought to mediate chromatin assembly in DNA replication and DNA repair. Assembles histone octamers onto replicating DNA in vitro. CAF-1 performs the first step of the nucleosome assembly process, bringing newly synthesized histones H3 and H4 to replicating DNA; histones H2A/H2B can bind to this chromatin precursor subsequent to DNA replication to complete the histone octamer. {ECO:0000269|PubMed:9813080}.;
- Pathway
- btg family proteins and cell cycle regulation
(Consensus)
Recessive Scores
- pRec
- 0.0832
Intolerance Scores
- loftool
- 0.333
- rvis_EVS
- 0.22
- rvis_percentile_EVS
- 68.44
Haploinsufficiency Scores
- pHI
- 0.666
- hipred
- Y
- hipred_score
- 0.773
- ghis
- 0.457
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.964
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Chaf1b
- Phenotype
Zebrafish Information Network
- Gene name
- chaf1b
- Affected structure
- retinal ganglion cell
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- DNA replication;DNA repair;nucleosome assembly;DNA replication-dependent nucleosome assembly;cell cycle;chromatin assembly
- Cellular component
- nuclear chromatin;nucleus;nucleoplasm;cytoplasm;cytosol;protein-containing complex;CAF-1 complex
- Molecular function
- chromatin binding;protein binding;histone binding;unfolded protein binding