DCAF17

DDB1 and CUL4 associated factor 17, the group of DDB1 and CUL4 associated factors

Basic information

Region (hg38): 2:171434217-171485052

Previous symbols: [ "C2orf37" ]

Links

ENSG00000115827 ∙ NCBI:80067 ∙ OMIM:612515 ∙ HGNC:25784 ∙ Uniprot:Q5H9S7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Woodhouse-Sakati syndrome (Limited), mode of inheritance: AR
• Woodhouse-Sakati syndrome (Strong), mode of inheritance: AR
• Woodhouse-Sakati syndrome (Strong), mode of inheritance: AR
• Woodhouse-Sakati syndrome (Strong), mode of inheritance: AR
• Woodhouse-Sakati syndrome (Supportive), mode of inheritance: AR
• Woodhouse-Sakati syndrome (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Woodhouse-Sakati syndrome	AR	Cardiovascular; Endocrine	Endocrine anomalies can include hypothyroidism and hypogonadism, and surveillance to allow appropriate medical care (eg, with replacement therapy, as well as care for manifestations such as diabetes mellitus) may be beneficial; Cardiac anomalies (including arrhythmia) have been reported, and surveillance and preventive measures may be beneficial; Awareness of hearing impairment may allow early interventions related to speech and language development	Audiologic/Otolaryngologic; Cardiovascular; Dermatologic; Endocrine; Neurologic	6876115; 7710875; 19026396; 18049083; 18175354; 20507343; 21963443; 21964978

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DCAF17 gene.

• Woodhouse-Sakati syndrome (25 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DCAF17 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				94	4	98
missense			85	12		97
nonsense	7					7
start loss	3					3
frameshift	14	3				17
inframe indel			1			1
splice donor/acceptor (+/-2bp)	1	9			3	13
splice region			4	29	4	37
non coding		1	59	112	47	219
Total	25	13	145	218	54

Highest pathogenic variant AF is 0.0000132

Variants in DCAF17

This is a list of pathogenic ClinVar variants found in the DCAF17 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-171434335-C-G		Woodhouse-Sakati syndrome	Uncertain significance (Jan 13, 2018)
2-171434346-C-T		Woodhouse-Sakati syndrome	Uncertain significance (Apr 27, 2017)
2-171434356-G-A		Woodhouse-Sakati syndrome	Uncertain significance (Jan 13, 2018)
2-171434365-C-T		Woodhouse-Sakati syndrome	Conflicting classifications of pathogenicity (Feb 24, 2020)
2-171434366-C-T		Woodhouse-Sakati syndrome	Uncertain significance (Jan 12, 2018)
2-171434372-C-G		Woodhouse-Sakati syndrome	Uncertain significance (Jan 13, 2018)
2-171434374-C-T		Woodhouse-Sakati syndrome	Uncertain significance (Jan 13, 2018)
2-171434380-T-C		Woodhouse-Sakati syndrome	Uncertain significance (Jan 12, 2018)
2-171434467-G-T		Woodhouse-Sakati syndrome	Uncertain significance (Jan 12, 2018)
2-171434569-C-G		Woodhouse-Sakati syndrome	Uncertain significance (Jan 13, 2018)
2-171434578-A-G		Woodhouse-Sakati syndrome	Pathogenic (Nov 17, 2023)
2-171434578-A-T		Woodhouse-Sakati syndrome	Pathogenic (Feb 03, 2023)
2-171434579-T-C		Woodhouse-Sakati syndrome	Pathogenic (Oct 23, 2023)
2-171434586-G-T		Woodhouse-Sakati syndrome	Likely benign (Aug 25, 2023)
2-171434593-A-C		Woodhouse-Sakati syndrome	Likely benign (Jan 29, 2024)
2-171434595-G-C		Inborn genetic diseases • Woodhouse-Sakati syndrome	Uncertain significance (May 30, 2022)
2-171434598-C-G		Woodhouse-Sakati syndrome	Likely benign (Oct 04, 2023)
2-171434598-C-T		Woodhouse-Sakati syndrome	Likely benign (Oct 27, 2023)
2-171434604-G-A		Woodhouse-Sakati syndrome	Conflicting classifications of pathogenicity (Jul 01, 2024)
2-171434604-G-T		Woodhouse-Sakati syndrome	Likely benign (Apr 17, 2023)
2-171434622-C-T		Woodhouse-Sakati syndrome	Likely benign (Jan 11, 2024)
2-171434625-G-A		Woodhouse-Sakati syndrome	Likely benign (Mar 19, 2023)
2-171434626-GC-G		Woodhouse-Sakati syndrome	Pathogenic (Dec 01, 2008)
2-171434628-G-A		Woodhouse-Sakati syndrome	Likely benign (Jun 23, 2023)
2-171434628-G-T		Woodhouse-Sakati syndrome • DCAF17-related disorder	Likely benign (Jan 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DCAF17	protein_coding	protein_coding	ENST00000375255	14	50836

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.74e-7	0.988	125714	0	34	125748	0.000135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.816	230	268	0.860	0.0000128	3387
Missense in Polyphen		80	101.56	0.78774		1314
Synonymous	0.562	84	90.8	0.925	0.00000420	974
Loss of Function	2.30	15	28.2	0.533	0.00000128	364

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000178	0.000178
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.000232	0.000231
European (Non-Finnish)	0.000186	0.000185
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.000218	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}.
• Pathway: Post-translational protein modification;Metabolism of proteins;Neddylation (Consensus)

Intolerance Scores

• loftool: 0.840
• rvis_EVS: -0.47
• rvis_percentile_EVS: 23.25

Haploinsufficiency Scores

• pHI: 0.0461
• hipred: Y
• hipred_score: 0.672
• ghis: 0.638

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.824

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dcaf17
• Phenotype: reproductive system phenotype; cellular phenotype

Gene ontology

• Biological process: protein ubiquitination;post-translational protein modification
• Cellular component: nucleoplasm;nucleolus;cytosol;integral component of membrane;Cul4-RING E3 ubiquitin ligase complex
• Molecular function: protein binding