DCAF4

DDB1 and CUL4 associated factor 4, the group of WD repeat domain containing|DDB1 and CUL4 associated factors

Basic information

Region (hg38): 14:72926376-72959703

Previous symbols: [ "WDR21", "WDR21A" ]

Links

ENSG00000119599 ∙ NCBI:26094 ∙ OMIM:616372 ∙ HGNC:20229 ∙ Uniprot:Q8WV16 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DCAF4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DCAF4 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					1	1
missense			33	5	1	39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	33	6	2

Variants in DCAF4

This is a list of pathogenic ClinVar variants found in the DCAF4 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
14-72937994-T-C		not specified	Uncertain significance (May 23, 2023)
14-72937999-G-C		not specified	Uncertain significance (Jul 13, 2021)
14-72938010-G-A		not specified	Uncertain significance (Feb 05, 2024)
14-72938055-G-A		not specified	Likely benign (Sep 14, 2022)
14-72938062-T-C			Benign (Apr 24, 2018)
14-72939869-T-G		not specified	Uncertain significance (Jan 10, 2022)
14-72940292-A-G		not specified	Uncertain significance (Oct 14, 2023)
14-72940316-G-A		not specified	Likely benign (Feb 28, 2024)
14-72940324-G-A		not specified	Uncertain significance (May 06, 2022)
14-72940345-C-T		not specified	Uncertain significance (Jun 06, 2023)
14-72940346-G-A		not specified	Likely benign (Mar 01, 2023)
14-72940358-A-G		not specified	Uncertain significance (Dec 17, 2021)
14-72941753-G-C		not specified	Uncertain significance (Sep 14, 2022)
14-72943047-G-A		not specified	Likely benign (Aug 15, 2023)
14-72945903-G-A		not specified	Uncertain significance (Apr 26, 2023)
14-72945918-A-C		not specified	Uncertain significance (Aug 17, 2021)
14-72946023-G-A		not specified	Uncertain significance (Sep 14, 2022)
14-72947143-T-C		not specified	Uncertain significance (Mar 02, 2023)
14-72947152-T-C		not specified	Uncertain significance (Jun 17, 2024)
14-72948525-G-A		Telomere length, mean leukocyte	Uncertain significance (Aug 03, 2016)
14-72951814-C-T		not specified	Uncertain significance (Jun 11, 2021)
14-72951865-A-C		not specified	Uncertain significance (Apr 07, 2023)
14-72951865-A-G		not specified	Uncertain significance (Jul 30, 2023)
14-72954205-G-A		not specified	Uncertain significance (Dec 07, 2023)
14-72954208-G-T		not specified	Uncertain significance (Dec 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DCAF4	protein_coding	protein_coding	ENST00000358377	13	33372

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000928	0.997	125696	0	51	125747	0.000203

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.420	294	315	0.933	0.0000205	3217
Missense in Polyphen		60	77.248	0.77672		877
Synonymous	0.390	120	126	0.956	0.00000824	976
Loss of Function	2.61	13	27.9	0.466	0.00000153	290

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000394	0.000394
Ashkenazi Jewish	0.00	0.00
East Asian	0.000441	0.000435
Finnish	0.0000934	0.0000924
European (Non-Finnish)	0.000229	0.000202
Middle Eastern	0.000441	0.000435
South Asian	0.000232	0.000229
Other	0.000490	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May function as a substrate receptor for CUL4-DDB1 E3 ubiquitin-protein ligase complex. {ECO:0000269|PubMed:16949367, ECO:0000269|PubMed:16964240}.
• Pathway: Post-translational protein modification;Metabolism of proteins;Neddylation (Consensus)

Recessive Scores

• pRec: 0.101

Intolerance Scores

• loftool: 0.908
• rvis_EVS: 1.34
• rvis_percentile_EVS: 94.29

Haploinsufficiency Scores

• pHI: 0.116
• hipred: N
• hipred_score: 0.377
• ghis: 0.474

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.585

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Dcaf4

Gene ontology

• Biological process: protein ubiquitination;post-translational protein modification
• Cellular component: nucleoplasm;Cul4-RING E3 ubiquitin ligase complex