WDR6

WD repeat domain 6, the group of WD repeat domain containing

Basic information

Region (hg38): 3:49007061-49015953

Links

ENSG00000178252 ∙ NCBI:11180 ∙ OMIM:606031 ∙ HGNC:12758 ∙ Uniprot:Q9NNW5 ∙ 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 WDR6 gene.

• Inborn genetic diseases (49 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WDR6 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				1		1
missense			44	2		46
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			3		1	4
Total	0	0	47	3	1

Variants in WDR6

This is a list of pathogenic ClinVar variants found in the WDR6 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-49007356-G-C			Likely benign (Mar 01, 2022)
3-49007427-T-G		not specified	Uncertain significance (Jul 13, 2021)
3-49011646-G-A		not specified	Uncertain significance (Jan 24, 2023)
3-49011739-C-T		not specified	Uncertain significance (Sep 12, 2023)
3-49011745-C-T		not specified	Uncertain significance (Mar 24, 2023)
3-49011860-G-A		not specified	Uncertain significance (May 30, 2023)
3-49011862-T-C		not specified	Uncertain significance (Jun 07, 2023)
3-49012050-G-T		not specified	Uncertain significance (Jun 02, 2023)
3-49012105-A-G		not specified	Likely benign (Jan 03, 2024)
3-49012157-A-G		not specified	Uncertain significance (Jan 26, 2023)
3-49012203-G-C		not specified	Uncertain significance (Oct 17, 2023)
3-49012231-G-T		not specified	Uncertain significance (Jan 24, 2024)
3-49012235-G-A		not specified	Uncertain significance (Apr 26, 2023)
3-49012312-C-T		not specified	Uncertain significance (Dec 19, 2023)
3-49012324-G-A		not specified	Uncertain significance (Oct 02, 2023)
3-49012429-C-T		not specified	Uncertain significance (Aug 09, 2021)
3-49012447-G-A		not specified	Uncertain significance (Nov 03, 2023)
3-49012484-G-C		not specified	Uncertain significance (Dec 08, 2021)
3-49012500-T-G		not specified	Uncertain significance (May 11, 2022)
3-49012547-C-T		not specified	Uncertain significance (Feb 06, 2023)
3-49012549-G-A		not specified	Uncertain significance (Jan 22, 2024)
3-49012591-G-A		not specified	Uncertain significance (Jan 23, 2024)
3-49012769-A-G		not specified	Uncertain significance (Jan 26, 2023)
3-49012780-C-T		not specified	Likely benign (Apr 06, 2022)
3-49012870-C-T		not specified	Uncertain significance (Mar 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WDR6	protein_coding	protein_coding	ENST00000395474	6	8892

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.14e-9	0.999	125671	0	77	125748	0.000306

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.799	631	690	0.914	0.0000421	7391
Missense in Polyphen		179	207.49	0.86267		2221
Synonymous	-0.144	277	274	1.01	0.0000151	2538
Loss of Function	2.87	21	40.8	0.515	0.00000268	387

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000536	0.000536
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000272	0.000272
Finnish	0.000186	0.000185
European (Non-Finnish)	0.000317	0.000316
Middle Eastern	0.000272	0.000272
South Asian	0.000460	0.000457
Other	0.000490	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Enhances the STK11/LKB1-induced cell growth suppression activity. Negative regulator of amino acid starvation-induced autophagy. {ECO:0000269|PubMed:17216128, ECO:0000269|PubMed:22354037}.

Recessive Scores

• pRec: 0.0981

Intolerance Scores

• loftool: 0.803
• rvis_EVS: -1.43
• rvis_percentile_EVS: 4.01

Haploinsufficiency Scores

• pHI: 0.0949
• hipred: N
• hipred_score: 0.372
• ghis: 0.655

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.577

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Wdr6

Gene ontology

• Biological process: cell cycle arrest;negative regulation of cell population proliferation;negative regulation of autophagy
• Cellular component: cytoplasm;cytosol;plasma membrane;COP9 signalosome
• Molecular function: RNA binding;protein binding