WDTC1

WD and tetratricopeptide repeats 1, the group of Tetratricopeptide repeat domain containing|WD repeat domain containing|DDB1 and CUL4 associated factors

Basic information

Region (hg38): 1:27234632-27308636

Links

ENSG00000142784 ∙ NCBI:23038 ∙ OMIM:619763 ∙ HGNC:29175 ∙ Uniprot:Q8N5D0 ∙ 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 WDTC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WDTC1 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					4	4
missense			23			23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	23	0	4

Variants in WDTC1

This is a list of pathogenic ClinVar variants found in the WDTC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-27261059-C-T		not specified	Uncertain significance (Apr 16, 2024)
1-27261060-G-A			Benign (Mar 29, 2018)
1-27261086-T-A		not specified	Uncertain significance (Dec 01, 2022)
1-27261088-C-T		not specified	Uncertain significance (Apr 26, 2024)
1-27263159-G-T		not specified	Uncertain significance (Apr 19, 2024)
1-27263177-G-A		not specified	Uncertain significance (Dec 17, 2023)
1-27263242-G-T			Benign (Apr 17, 2018)
1-27287798-G-A		not specified	Uncertain significance (Apr 01, 2024)
1-27292246-T-G		not specified	Uncertain significance (Dec 27, 2022)
1-27294617-G-T		not specified	Uncertain significance (Aug 12, 2021)
1-27294619-G-C		not specified	Uncertain significance (Jan 10, 2023)
1-27296341-T-A		not specified	Uncertain significance (Jul 06, 2021)
1-27296373-C-T			Benign (May 17, 2018)
1-27297076-C-T			Benign (Dec 11, 2017)
1-27297099-A-G		not specified	Uncertain significance (Apr 13, 2023)
1-27297128-C-T		not specified	Uncertain significance (Nov 08, 2022)
1-27297129-G-A		not specified	Uncertain significance (Feb 15, 2023)
1-27297135-C-T		not specified	Uncertain significance (Sep 01, 2021)
1-27297968-G-C		not specified	Uncertain significance (Oct 22, 2021)
1-27298061-C-A		not specified	Uncertain significance (Feb 27, 2024)
1-27301423-G-A		not specified	Uncertain significance (Jun 16, 2024)
1-27303648-C-T		not specified	Uncertain significance (Sep 20, 2023)
1-27303656-C-T		not specified	Uncertain significance (Aug 30, 2021)
1-27303662-C-T		not specified	Uncertain significance (Mar 06, 2023)
1-27303669-C-T		not specified	Uncertain significance (Aug 10, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WDTC1	protein_coding	protein_coding	ENST00000361771	15	74104

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000849	125738	0	4	125742	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.81	209	432	0.484	0.0000275	4457
Missense in Polyphen		42	168.11	0.24983		1679
Synonymous	0.638	162	173	0.938	0.0000110	1323
Loss of Function	4.90	3	33.7	0.0891	0.00000175	374

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000677	0.0000544
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.00000879	0.00000879
Middle Eastern	0.0000677	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May function as a substrate receptor for CUL4-DDB1 E3 ubiquitin-protein ligase complex. {ECO:0000269|PubMed:16964240}.
• Pathway: Post-translational protein modification;Metabolism of proteins;Neddylation (Consensus)

Recessive Scores

• pRec: 0.149

Intolerance Scores

• loftool: 0.0872
• rvis_EVS: -0.44
• rvis_percentile_EVS: 24.46

Haploinsufficiency Scores

• pHI: 0.987
• hipred: Y
• hipred_score: 0.825
• ghis: 0.529

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.985

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Wdtc1
• Phenotype: growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); homeostasis/metabolism 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); hearing/vestibular/ear phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;in utero embryonic development;glucose metabolic process;regulation of cell size;protein ubiquitination;cellular response to insulin stimulus;multicellular organism growth;negative regulation of catalytic activity;post-translational protein modification;negative regulation of fatty acid biosynthetic process;cellular chemical homeostasis
• Cellular component: nucleoplasm;cytosol
• Molecular function: enzyme inhibitor activity;protein binding;histone binding;histone deacetylase binding