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.

not_specified (52 variants)
not_provided (5 variants)

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. These statistics are base on transcript: NM_001276252.2. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous					4 clinvar	4
missense			52 clinvar			52
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	52	0	4

Loading clinvar variants...

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