DCAF4L2

DDB1 and CUL4 associated factor 4 like 2, the group of WD repeat domain containing

Basic information

Region (hg38): 8:87870747-87874015

Previous symbols: [ "WDR21C" ]

Links

ENSG00000176566 ∙ NCBI:138009 ∙ ∙ HGNC:26657 ∙ Uniprot:Q8NA75 ∙ 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 DCAF4L2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DCAF4L2 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				6	2	8
missense			21	1	3	25
nonsense						0
start loss						0
frameshift						0
inframe indel				1		1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	8	5

Variants in DCAF4L2

This is a list of pathogenic ClinVar variants found in the DCAF4L2 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-87872830-A-T		not specified	Uncertain significance (Feb 10, 2023)
8-87872875-A-G		not specified	Uncertain significance (Mar 25, 2024)
8-87872882-G-T		not specified	Uncertain significance (Jul 20, 2021)
8-87872889-G-A		DCAF4L2-related disorder	Likely benign (Dec 06, 2019)
8-87872964-G-A		DCAF4L2-related disorder	Likely benign (Feb 25, 2019)
8-87872992-CCTT-C		DCAF4L2-related disorder	Likely benign (Feb 01, 2023)
8-87872995-T-C		not specified	Uncertain significance (Nov 01, 2022)
8-87873028-G-A		DCAF4L2-related disorder	Benign (May 02, 2019)
8-87873034-T-C		DCAF4L2-related disorder	Benign (Feb 23, 2019)
8-87873036-C-T		DCAF4L2-related disorder	Likely benign (Oct 28, 2019)
8-87873126-G-A		DCAF4L2-related disorder	Likely benign (Sep 19, 2019)
8-87873137-G-A		DCAF4L2-related disorder	Benign (May 02, 2019)
8-87873146-G-A		DCAF4L2-related disorder	Likely benign (Jul 25, 2019)
8-87873172-A-T		not specified	Uncertain significance (Sep 29, 2022)
8-87873205-C-T		not specified	Uncertain significance (May 23, 2024)
8-87873211-C-T		not specified	Uncertain significance (Mar 31, 2023)
8-87873229-A-T		not specified	Uncertain significance (Sep 03, 2024)
8-87873266-T-C		not specified	Uncertain significance (Dec 06, 2023)
8-87873272-T-C		not specified	Uncertain significance (Jun 12, 2023)
8-87873328-G-A		not specified	Uncertain significance (Nov 09, 2023)
8-87873336-G-A		DCAF4L2-related disorder	Likely benign (May 24, 2019)
8-87873346-A-T		not specified	Uncertain significance (Aug 08, 2022)
8-87873364-C-T		not specified	Uncertain significance (May 23, 2023)
8-87873397-A-C		not specified	Uncertain significance (Nov 30, 2022)
8-87873398-G-C		not specified	Uncertain significance (Jul 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DCAF4L2	protein_coding	protein_coding	ENST00000319675	1	3324

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0857	234	238	0.984	0.0000154	2553
Missense in Polyphen		54	61.507	0.87794		715
Synonymous	-1.15	118	103	1.14	0.00000744	839
Loss of Function

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish
East Asian
Finnish
European (Non-Finnish)
Middle Eastern
South Asian
Other

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0981

Intolerance Scores

• loftool: 0.776
• rvis_EVS: 0
• rvis_percentile_EVS: 53.85

Haploinsufficiency Scores

• pHI: 0.154
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0818

Gene Damage Prediction

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