DCAF12L1

DDB1 and CUL4 associated factor 12 like 1, the group of WD repeat domain containing

Basic information

Region (hg38): X:126549383-126552814

Previous symbols: [ "WDR40B" ]

Links

ENSG00000198889 ∙ NCBI:139170 ∙ ∙ HGNC:29395 ∙ Uniprot:Q5VU92 ∙ 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 DCAF12L1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DCAF12L1 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				3	3	6
missense			15	1		16
nonsense						0
start loss						0
frameshift		1				1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	1	15	4	3

Variants in DCAF12L1

This is a list of pathogenic ClinVar variants found in the DCAF12L1 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-126551246-G-A		not specified	Uncertain significance (Sep 14, 2022)
X-126551422-C-G		not specified	Uncertain significance (Jan 24, 2024)
X-126551472-G-A			Benign (Dec 31, 2019)
X-126551530-C-T		not specified	Uncertain significance (Jun 11, 2021)
X-126551600-C-T			Likely benign (-)
X-126551659-T-C		not specified	Uncertain significance (Oct 22, 2024)
X-126551729-C-T		not specified	Likely benign (May 20, 2024)
X-126551794-C-T		not specified	Uncertain significance (Nov 13, 2024)
X-126551814-C-A			Likely benign (Jul 01, 2022)
X-126551852-T-C		not specified	Uncertain significance (Dec 12, 2024)
X-126551915-C-A		not specified	Uncertain significance (Sep 08, 2024)
X-126552012-G-T			Likely benign (Mar 01, 2023)
X-126552048-C-T			Likely benign (Jan 01, 2023)
X-126552145-A-G		not specified	Uncertain significance (Jun 16, 2024)
X-126552201-CAA-C		Male infertility with azoospermia or oligozoospermia due to single gene mutation	Likely pathogenic (Sep 01, 2023)
X-126552217-G-C		not specified	Uncertain significance (Aug 12, 2021)
X-126552226-C-T		not specified	Uncertain significance (Jan 26, 2025)
X-126552323-T-C		not specified	Uncertain significance (Dec 10, 2024)
X-126552369-T-G			Benign (May 30, 2018)
X-126552372-C-G			Benign (May 30, 2018)
X-126552379-C-T		not specified	Uncertain significance (May 05, 2023)
X-126552400-C-T		not specified	Uncertain significance (Sep 20, 2023)
X-126552455-C-T		not specified	Uncertain significance (Feb 11, 2025)
X-126552550-G-A		not specified	Uncertain significance (Jun 16, 2023)
X-126552554-C-T		not specified	Uncertain significance (Oct 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DCAF12L1	protein_coding	protein_coding	ENST00000371126	1	3466

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.954	0.0458	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.41	125	227	0.550	0.0000205	2973
Missense in Polyphen		11	71.229	0.15443		983
Synonymous	0.113	114	116	0.987	0.0000112	1019
Loss of Function	2.88	0	9.67	0.00	6.73e-7	135

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)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: -0.34
• rvis_percentile_EVS: 30.37

Haploinsufficiency Scores

• pHI: 0.167
• hipred: N
• hipred_score: 0.290
• ghis: 0.430

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dcaf12l1

Gene ontology

• Biological process: biological_process
• Cellular component: cellular_component;Cul4-RING E3 ubiquitin ligase complex
• Molecular function: molecular_function;protein binding