DCAF12L2

DDB1 and CUL4 associated factor 12 like 2, the group of WD repeat domain containing

Basic information

Region (hg38): X:126163499-126166289

Previous symbols: [ "WDR40C" ]

Links

ENSG00000198354 ∙ NCBI:340578 ∙ ∙ HGNC:32950 ∙ Uniprot:Q5VW00 ∙ 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 DCAF12L2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DCAF12L2 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			22			22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	0	0

Variants in DCAF12L2

This is a list of pathogenic ClinVar variants found in the DCAF12L2 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-126164544-G-C		not specified	Uncertain significance (Apr 22, 2022)
X-126164639-T-C		not specified	Uncertain significance (Apr 04, 2024)
X-126164688-G-T		not specified	Uncertain significance (Feb 22, 2024)
X-126164691-T-G		not specified	Uncertain significance (Aug 28, 2024)
X-126164741-G-A		not specified	Uncertain significance (Dec 15, 2023)
X-126164786-T-C		not specified	Uncertain significance (Jul 27, 2021)
X-126164880-C-T		not specified	Uncertain significance (Dec 20, 2022)
X-126164928-C-T		not specified	Uncertain significance (Aug 28, 2024)
X-126164937-A-T		not specified	Uncertain significance (Sep 29, 2023)
X-126164941-G-C		not specified	Uncertain significance (Nov 14, 2023)
X-126164957-A-C		not specified	Uncertain significance (Feb 28, 2023)
X-126164997-C-T		not specified	Uncertain significance (May 24, 2024)
X-126165114-T-C		not specified	Conflicting classifications of pathogenicity (Feb 08, 2023)
X-126165116-A-C		not specified	Conflicting classifications of pathogenicity (Feb 08, 2023)
X-126165146-G-C		not specified	Uncertain significance (Jul 14, 2024)
X-126165198-C-A		not specified	Uncertain significance (May 16, 2024)
X-126165218-T-A		not specified	Uncertain significance (Apr 27, 2023)
X-126165225-G-A		not specified	Uncertain significance (Jan 02, 2024)
X-126165295-G-T		not specified	Uncertain significance (Oct 29, 2021)
X-126165296-C-G		not specified	Uncertain significance (Nov 10, 2022)
X-126165360-C-T		not specified	Uncertain significance (Aug 20, 2024)
X-126165376-G-C		not specified	Uncertain significance (Feb 06, 2024)
X-126165395-T-C		not specified	Uncertain significance (Aug 13, 2021)
X-126165521-A-C		not specified	Uncertain significance (Aug 12, 2021)
X-126165533-G-A		not specified	Uncertain significance (Jun 18, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DCAF12L2	protein_coding	protein_coding	ENST00000538699	1	1744

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00587	0.912	125720	5	8	125733	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.937	186	226	0.824	0.0000201	2971
Missense in Polyphen		44	65.896	0.66771		948
Synonymous	0.724	100	110	0.912	0.0000104	1029
Loss of Function	1.49	5	10.1	0.495	7.75e-7	133

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000146	0.000146
Ashkenazi Jewish	0.000401	0.000298
East Asian	0.0000723	0.0000544
Finnish	0.0000626	0.0000462
European (Non-Finnish)	0.0000367	0.0000264
Middle Eastern	0.0000723	0.0000544
South Asian	0.0000535	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.270
• rvis_EVS: -0.23
• rvis_percentile_EVS: 37.32

Haploinsufficiency Scores

• pHI: 0.537
• hipred: N
• hipred_score: 0.269
• ghis: 0.499

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: 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: Dcaf12l2

Gene ontology

• Cellular component: Cul4-RING E3 ubiquitin ligase complex