DCAF12

DDB1 and CUL4 associated factor 12, the group of WD repeat domain containing|DDB1 and CUL4 associated factors

Basic information

Region (hg38): 9:34086386-34127399

Previous symbols: [ "KIAA1892", "WDR40A" ]

Links

ENSG00000198876 ∙ NCBI:25853 ∙ OMIM:620087 ∙ HGNC:19911 ∙ Uniprot:Q5T6F0 ∙ 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 DCAF12 gene.

• Inborn genetic diseases (14 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DCAF12 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			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	1	0

Variants in DCAF12

This is a list of pathogenic ClinVar variants found in the DCAF12 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-34088366-G-A		not specified	Uncertain significance (Jun 16, 2023)
9-34088496-T-C		not specified	Uncertain significance (Nov 17, 2023)
9-34089506-T-C		not specified	Uncertain significance (Mar 07, 2024)
9-34089516-T-A		not specified	Uncertain significance (Oct 05, 2021)
9-34093358-G-A		not specified	Uncertain significance (Sep 23, 2023)
9-34096752-G-A			Likely benign (Jun 23, 2018)
9-34098454-G-C		not specified	Uncertain significance (May 30, 2023)
9-34098464-T-C		not specified	Uncertain significance (Aug 14, 2023)
9-34098479-C-T		not specified	Uncertain significance (Feb 06, 2024)
9-34098500-T-C		not specified	Uncertain significance (Apr 10, 2023)
9-34106482-C-T		not specified	Uncertain significance (Jan 16, 2024)
9-34106484-T-C		not specified	Uncertain significance (Jan 16, 2024)
9-34106494-C-T		not specified	Uncertain significance (Mar 01, 2024)
9-34107396-T-C		not specified	Uncertain significance (Mar 31, 2023)
9-34107456-A-C		not specified	Uncertain significance (Jan 04, 2022)
9-34125058-G-A		not specified	Uncertain significance (Dec 05, 2022)
9-34125151-C-G		not specified	Uncertain significance (Feb 03, 2022)
9-34125155-C-G		not specified	Uncertain significance (Jan 30, 2024)
9-34125163-G-C		not specified	Uncertain significance (Feb 16, 2023)
9-34125241-G-C		not specified	Uncertain significance (Dec 21, 2022)
9-34126356-G-C		not specified	Uncertain significance (Dec 23, 2022)
9-34126379-G-C		not specified	Uncertain significance (Dec 19, 2022)
9-34126424-C-T		not specified	Uncertain significance (Sep 28, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DCAF12	protein_coding	protein_coding	ENST00000361264	9	41013

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000219	0.977	125726	0	22	125748	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.55	184	253	0.727	0.0000134	2920
Missense in Polyphen		45	84.549	0.53224		987
Synonymous	0.783	91	101	0.901	0.00000534	920
Loss of Function	2.09	13	24.1	0.540	0.00000130	265

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000271	0.000271
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000794	0.0000791
Middle Eastern	0.00	0.00
South Asian	0.000131	0.000131
Other	0.000163	0.000163

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}.

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.648
• rvis_EVS: -0.38
• rvis_percentile_EVS: 27.69

Haploinsufficiency Scores

• pHI: 0.555
• hipred: Y
• hipred_score: 0.756
• ghis: 0.564

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dcaf12

Gene ontology

• Biological process: protein ubiquitination
• Cellular component: cytoplasm;centrosome;Cul4-RING E3 ubiquitin ligase complex
• Molecular function: protein binding