CHAF1A
Basic information
Region (hg38): 19:4402640-4445018
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (122 variants)
- Craniofacial_microsomia (6 variants)
- not_provided (5 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHAF1A gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005483.3. 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 | 2 | |||||
| missense | 116 | 124 | ||||
| nonsense | 1 | |||||
| start loss | 0 | |||||
| frameshift | 3 | |||||
| splice donor/acceptor (+/-2bp) | 2 | |||||
| Total | 0 | 6 | 117 | 8 | 1 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CHAF1A | protein_coding | protein_coding | ENST00000301280 | 15 | 42357 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 0.00000284 | 125743 | 0 | 4 | 125747 | 0.0000159 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.85 | 458 | 584 | 0.785 | 0.0000373 | 6282 |
| Missense in Polyphen | 94 | 166.82 | 0.56347 | 1743 | ||
| Synonymous | -0.909 | 269 | 251 | 1.07 | 0.0000180 | 1839 |
| Loss of Function | 5.72 | 1 | 40.1 | 0.0249 | 0.00000189 | 509 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000268 | 0.0000264 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Core component of the CAF-1 complex, a complex 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. CHAF1A binds to histones H3 and H4. It may play a role in heterochromatin maintenance in proliferating cells by bringing newly synthesized cbx proteins to heterochromatic DNA replication foci (By similarity). {ECO:0000250, ECO:0000269|PubMed:15327775}.;
- Pathway
- miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;Nanoparticle triggered autophagic cell death;btg family proteins and cell cycle regulation
(Consensus)
Recessive Scores
- pRec
- 0.113
Intolerance Scores
- loftool
- 0.126
- rvis_EVS
- 0.32
- rvis_percentile_EVS
- 72.85
Haploinsufficiency Scores
- pHI
- 0.925
- hipred
- Y
- hipred_score
- 0.734
- ghis
- 0.574
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.972
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Chaf1a
- Phenotype
- embryo 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); cellular phenotype;
Gene ontology
- Biological process
- DNA replication;DNA repair;nucleosome assembly;DNA replication-dependent nucleosome assembly;cell cycle;chromatin assembly
- Cellular component
- nuclear chromatin;nucleus;protein-containing complex;CAF-1 complex
- Molecular function
- chromatin binding;protein binding;identical protein binding;unfolded protein binding;chromo shadow domain binding