DCAF1
DDB1 and CUL4 associated factor 1, the group of DDB1 and CUL4 associated factors|Armadillo like helical domain containing
Basic information
Region (hg38): 3:51395867-51500015
Previous symbols: [ "VPRBP" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
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 DCAF1 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 | 2 | |||||
| missense | 0 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 0 | 2 | 0 |
Variants in DCAF1
This is a list of pathogenic ClinVar variants found in the DCAF1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 3-51403261-A-G | Likely benign (Apr 01, 2022) | |||
| 3-51420750-G-A | Likely benign (Apr 01, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| DCAF1 | protein_coding | protein_coding | ENST00000423656 | 15 | 100713 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 8.44e-7 | 124636 | 0 | 2 | 124638 | 0.00000802 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 4.84 | 262 | 594 | 0.441 | 0.0000331 | 7117 |
| Missense in Polyphen | 27 | 152.87 | 0.17662 | 1870 | ||
| Synonymous | 0.913 | 207 | 224 | 0.922 | 0.0000120 | 2124 |
| Loss of Function | 5.96 | 1 | 43.4 | 0.0231 | 0.00000247 | 525 |
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) | 0.00000885 | 0.00000885 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000337 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Acts both as a substrate recognition component of E3 ubiquitin-protein ligase complexes and as an atypical serine/threonine-protein kinase, playing key roles in various processes such as cell cycle, telomerase regulation and histone modification. Probable substrate-specific adapter of a DCX (DDB1- CUL4-X-box) E3 ubiquitin-protein ligase complex, named CUL4A-RBX1- DDB1-DCAF1/VPRBP complex, which mediates ubiquitination and proteasome-dependent degradation of proteins such as NF2. Involved in the turnover of methylated proteins: recognizes and binds methylated proteins via its chromo domain, leading to ubiquitination of target proteins by the RBX1-DDB1-DCAF1/VPRBP complex (PubMed:23063525). The CUL4A-RBX1-DDB1-DCAF1/VPRBP complex is also involved in B-cell development: DCAF1 is recruited by RAG1 to ubiquitinate proteins, leading to limit error-prone repair during V(D)J recombination. Also part of the EDVP complex, an E3 ligase complex that mediates ubiquitination of proteins such as TERT, leading to TERT degradation and telomerase inhibition (PubMed:23362280). Also acts as an atypical serine/threonine- protein kinase that specifically mediates phosphorylation of 'Thr- 120' of histone H2A (H2AT120ph) in a nucleosomal context, thereby repressing transcription. H2AT120ph is present in the regulatory region of many tumor suppresor genes, down-regulates their transcription and is present at high level in a number of tumors (PubMed:24140421). Involved in JNK-mediated apoptosis during cell competition process via its interaction with LLGL1 and LLGL2 (PubMed:20644714). {ECO:0000269|PubMed:16964240, ECO:0000269|PubMed:17609381, ECO:0000269|PubMed:17630831, ECO:0000269|PubMed:18332868, ECO:0000269|PubMed:18524771, ECO:0000269|PubMed:18606781, ECO:0000269|PubMed:19287380, ECO:0000269|PubMed:20644714, ECO:0000269|PubMed:22184063, ECO:0000269|PubMed:23063525, ECO:0000269|PubMed:23362280, ECO:0000269|PubMed:24140421}.; FUNCTION: (Microbial infection) In case of infection by HIV-2 virus, it is recruited by HIV-2 Vpx in order to hijack the CUL4A- RBX1-DDB1-DCAF1/VPRBP function leading to enhanced efficiency of macrophage infection and promotion of the replication of cognate primate lentiviruses in cells of monocyte/macrophage lineage. {ECO:0000269|PubMed:17314515, ECO:0000269|PubMed:18464893, ECO:0000269|PubMed:19264781, ECO:0000269|PubMed:19923175, ECO:0000269|PubMed:24336198}.;
- Pathway
- Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation
(Consensus)
Recessive Scores
- pRec
- 0.0960
Haploinsufficiency Scores
- pHI
- 0.0832
- hipred
- hipred_score
- ghis
- 0.545
Mouse Genome Informatics
- Gene name
- Dcaf1
- 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
- negative regulation of transcription by RNA polymerase II;viral process;protein ubiquitination;B cell differentiation;V(D)J recombination;cell competition in a multicellular organism;histone H2A-T120 phosphorylation
- Cellular component
- fibrillar center;nucleus;cytoplasm;COP9 signalosome;Cul4-RING E3 ubiquitin ligase complex
- Molecular function
- protein binding;ATP binding;estrogen receptor binding;histone kinase activity (H2A-T120 specific)