WDR46

WD repeat domain 46, the group of MicroRNA protein coding host genes|SSU processome|WD repeat domain containing

Basic information

Region (hg38): 6:33279108-33289247

Previous symbols: [ "C6orf11" ]

Links

ENSG00000227057 ∙ NCBI:9277 ∙ OMIM:611440 ∙ HGNC:13923 ∙ Uniprot:O15213 ∙ 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 WDR46 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WDR46 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			33			33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	33	0	0

Variants in WDR46

This is a list of pathogenic ClinVar variants found in the WDR46 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-33279308-G-A		not specified	Uncertain significance (Feb 16, 2023)
6-33279308-G-C		not specified	Uncertain significance (Nov 08, 2021)
6-33279328-T-C		not specified	Uncertain significance (Oct 29, 2021)
6-33279331-G-A		not specified	Uncertain significance (Jun 07, 2023)
6-33279334-T-G		not specified	Uncertain significance (Mar 06, 2023)
6-33279338-T-C		not specified	Uncertain significance (Mar 06, 2023)
6-33279357-G-C		not specified	Uncertain significance (Dec 18, 2023)
6-33279508-C-T		not specified	Uncertain significance (Nov 24, 2021)
6-33279591-T-C		not specified	Uncertain significance (Oct 03, 2023)
6-33279828-C-T		not specified	Uncertain significance (Nov 17, 2022)
6-33280517-C-T		not specified	Uncertain significance (Jan 23, 2024)
6-33280727-T-G		not specified	Uncertain significance (Jul 12, 2023)
6-33280769-C-T		not specified	Uncertain significance (Jul 14, 2021)
6-33280815-C-G		not specified	Uncertain significance (Jun 10, 2024)
6-33280853-G-A		not specified	Uncertain significance (Feb 12, 2024)
6-33280904-A-G		not specified	Uncertain significance (Aug 24, 2022)
6-33280976-G-A		not specified	Uncertain significance (Jan 17, 2024)
6-33287093-T-C		not specified	Uncertain significance (Aug 10, 2021)
6-33287135-C-T		not specified	Uncertain significance (Mar 31, 2024)
6-33287142-C-T		not specified	Uncertain significance (Oct 12, 2021)
6-33287180-A-G		not specified	Uncertain significance (Jun 18, 2021)
6-33287356-G-A		not specified	Uncertain significance (May 25, 2022)
6-33287393-G-A		not specified	Uncertain significance (Mar 29, 2023)
6-33287396-G-A		not specified	Uncertain significance (Aug 24, 2022)
6-33287417-G-A		not specified	Uncertain significance (Oct 22, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WDR46	protein_coding	protein_coding	ENST00000374617	15	10420

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.43e-13	0.798	125669	0	79	125748	0.000314

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.861	320	366	0.873	0.0000215	3923
Missense in Polyphen		97	135.29	0.71698		1522
Synonymous	1.44	116	138	0.844	0.00000727	1255
Loss of Function	1.81	25	36.9	0.678	0.00000228	363

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000659	0.000659
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000459	0.000440
Middle Eastern	0.000163	0.000163
South Asian	0.000261	0.000261
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Scaffold component of the nucleolar structure. Required for localization of DDX21 and NCL to the granular compartment of the nucleolus. {ECO:0000269|PubMed:23848194}.
• Pathway: rRNA processing;Metabolism of RNA;rRNA modification in the nucleus and cytosol;rRNA processing in the nucleus and cytosol (Consensus)

Intolerance Scores

• loftool: 0.900
• rvis_EVS: -0.09
• rvis_percentile_EVS: 46.92

Haploinsufficiency Scores

• pHI: 0.124
• hipred: N
• hipred_score: 0.428
• ghis: 0.535

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0773

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Wdr46

Zebrafish Information Network

• Gene name: wdr46
• Affected structure: trunk
• Phenotype tag: abnormal
• Phenotype quality: decreased thickness

Gene ontology

• Biological process: maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA);rRNA processing
• Cellular component: cellular_component;nucleoplasm;nucleolus;small-subunit processome
• Molecular function: RNA binding