DCAF16

DDB1 and CUL4 associated factor 16, the group of DDB1 and CUL4 associated factors

Basic information

Region (hg38): 4:17800655-17810758

Previous symbols: [ "C4orf30" ]

Links

ENSG00000163257 ∙ NCBI:54876 ∙ ∙ HGNC:25987 ∙ Uniprot:Q9NXF7 ∙ 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 DCAF16 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DCAF16 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						0
missense			19			19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	0	0

Variants in DCAF16

This is a list of pathogenic ClinVar variants found in the DCAF16 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-17803546-T-G		not specified	Uncertain significance (Aug 01, 2024)
4-17803549-G-A		not specified	Uncertain significance (Sep 17, 2021)
4-17803553-T-C		not specified	Uncertain significance (Feb 05, 2024)
4-17803561-G-A		not specified	Uncertain significance (May 26, 2024)
4-17803664-T-G		not specified	Uncertain significance (May 25, 2022)
4-17803712-C-T		not specified	Uncertain significance (Mar 04, 2024)
4-17803729-T-C		not specified	Uncertain significance (Feb 27, 2025)
4-17803759-A-G		not specified	Uncertain significance (Oct 12, 2022)
4-17803780-A-T		not specified	Uncertain significance (Feb 15, 2023)
4-17803805-A-G		not specified	Uncertain significance (Nov 13, 2023)
4-17803854-T-G		not specified	Uncertain significance (May 01, 2024)
4-17803864-A-G		not specified	Uncertain significance (Jan 08, 2024)
4-17803865-T-C		not specified	Uncertain significance (Jun 30, 2023)
4-17803994-C-T		not specified	Uncertain significance (Jul 22, 2022)
4-17804002-G-A		not specified	Uncertain significance (Jun 01, 2023)
4-17804030-C-T		not specified	Uncertain significance (Mar 25, 2024)
4-17804051-C-T		not specified	Uncertain significance (Dec 18, 2023)
4-17804061-C-G		not specified	Uncertain significance (Jul 07, 2024)
4-17804094-A-C		not specified	Uncertain significance (Dec 08, 2023)
4-17804116-T-A		not specified	Uncertain significance (Jan 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DCAF16	protein_coding	protein_coding	ENST00000382247	1	10104

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000329	0.609	125730	0	17	125747	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0391	105	106	0.989	0.00000522	1380
Missense in Polyphen		20	20.073	0.99637		242
Synonymous	-1.19	50	40.4	1.24	0.00000187	449
Loss of Function	0.625	6	7.89	0.760	4.92e-7	86

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000116	0.000116
Ashkenazi Jewish	0.00	0.00
East Asian	0.000217	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.0000353	0.0000352
Middle Eastern	0.000217	0.000217
South Asian	0.000196	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

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

Intolerance Scores

• loftool: 0.569
• rvis_EVS: 0.13
• rvis_percentile_EVS: 63

Haploinsufficiency Scores

• pHI: 0.216
• hipred: Y
• hipred_score: 0.578
• ghis: 0.585

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.914

Gene Damage Prediction

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

Gene ontology

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