DCAF13

DDB1 and CUL4 associated factor 13, the group of SSU processome|DDB1 and CUL4 associated factors|WD repeat domain containing

Basic information

Region (hg38): 8:103414713-103443453

Previous symbols: [ "WDSOF1" ]

Links

ENSG00000164934 ∙ NCBI:25879 ∙ OMIM:616196 ∙ HGNC:24535 ∙ Uniprot:Q9NV06 ∙ 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 DCAF13 gene.

• Inborn genetic diseases (25 variants)
• not provided (22 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DCAF13 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	2
missense			21	1	3	25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			8	10		18
Total	0	0	29	11	5

Variants in DCAF13

This is a list of pathogenic ClinVar variants found in the DCAF13 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-103414765-T-A			Likely benign (Apr 20, 2022)
8-103414769-T-C			Likely benign (Dec 20, 2022)
8-103414770-G-A			Likely benign (Aug 23, 2023)
8-103414770-G-T			Likely benign (Dec 20, 2023)
8-103414772-G-GCC			Likely benign (Mar 10, 2023)
8-103414777-C-A			Likely benign (Dec 03, 2021)
8-103414777-C-T			Likely benign (Oct 17, 2022)
8-103414781-T-TA			Uncertain significance (May 22, 2023)
8-103414790-A-G			Uncertain significance (Jan 18, 2024)
8-103414809-G-A		SLC25A32-related disorder	Likely benign (Sep 17, 2019)
8-103414822-G-A		not specified	Uncertain significance (Oct 05, 2023)
8-103414823-C-A			Likely benign (Jan 06, 2024)
8-103414835-A-C		not specified	Uncertain significance (Oct 27, 2021)
8-103414841-C-G			Uncertain significance (Dec 07, 2023)
8-103414850-C-A			Uncertain significance (Apr 24, 2023)
8-103414854-C-T			Likely benign (Aug 27, 2023)
8-103414874-G-A		not specified	Uncertain significance (Jun 15, 2023)
8-103414875-G-C			Likely benign (Jul 26, 2022)
8-103414876-A-C		not specified	Uncertain significance (Aug 28, 2023)
8-103414878-G-A			Likely benign (Jul 27, 2022)
8-103414903-G-A		not specified	Uncertain significance (Dec 08, 2023)
8-103414910-C-T			Uncertain significance (Apr 10, 2023)
8-103414918-G-T			Uncertain significance (Dec 24, 2022)
8-103414919-A-ACTGGCC			Uncertain significance (May 11, 2022)
8-103414929-G-A			Likely benign (Oct 09, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DCAF13	protein_coding	protein_coding	ENST00000297579	11	28740

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.94e-10	0.977	125695	0	52	125747	0.000207

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.689	382	346	1.10	0.0000179	3896
Missense in Polyphen		80	95.087	0.84134		1152
Synonymous	-1.41	138	119	1.16	0.00000571	1143
Loss of Function	2.24	20	34.1	0.587	0.00000221	344

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000332	0.000313
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.000332	0.000326
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000249	0.000246
Middle Eastern	0.000332	0.000326
South Asian	0.000209	0.000196
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Possible role in ribosomal RNA processing (By similarity). May function as a substrate receptor for CUL4-DDB1 E3 ubiquitin-protein ligase complex. {ECO:0000250, ECO:0000269|PubMed:16949367}.
• Pathway: rRNA processing;Post-translational protein modification;Metabolism of proteins;Metabolism of RNA;Neddylation;rRNA modification in the nucleus and cytosol;rRNA processing in the nucleus and cytosol (Consensus)

Recessive Scores

• pRec: 0.0897

Intolerance Scores

• loftool: 0.883
• rvis_EVS: 0.85
• rvis_percentile_EVS: 88.48

Haploinsufficiency Scores

• pHI: 0.874
• hipred: Y
• hipred_score: 0.629
• ghis: 0.586

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: H
• gene_indispensability_pred: N
• gene_indispensability_score: 0.478

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dcaf13
• 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); embryo phenotype

Gene ontology

• Biological process: maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA);rRNA processing;protein ubiquitination;post-translational protein modification
• Cellular component: nucleus;nucleoplasm;nucleolus;centrosome;cytosol;cell junction;small-subunit processome;Cul4-RING E3 ubiquitin ligase complex
• Molecular function: RNA binding;estrogen receptor binding