WDR46

protein-coding

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

Gene summary

Enables RNA binding activity. Involved in ribosomal small subunit biogenesis. Located in nucleolus. Part of small-subunit processome. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C6orf11

MANE transcript

NM_005452.6

Inheritance

—

ClinVar variants

U:102B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.68

Max pathogenic AF

—

Genomic locus

chr6:33,279,108-33,289,247

External References & Databases

Ensembl (ENSG00000227057)

Transcript & Mutation Effects

hg38 • Region Span ~10.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to WDR46 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 92

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_005452.6. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			92 clinvar	3 clinvar		95
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			10 clinvar			10
Total	0	0	102	3	0	105

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 11 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_005452.6	RefSeq	NP_005443.3	15	MANE Select
ENST00000374617.9	Ensembl	ENSP00000363746.4	15	MANE Select
NM_001164267.2	RefSeq	NP_001157739.1	15	Standard
ENST00000444176.1	Ensembl	ENSP00000405568.1	10	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
wdr46	Danio rerio	Structure: trunk Quality: decreased thickness abnormal

Gene / Model

Organism

Observed Phenotype

wdr46

Danio rerio

Structure: trunk

Quality: decreased thickness

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

rRNA processing
Metabolism of RNA
rRNA modification in the nucleus and cytosol
rRNA processing in the nucleus and cytosol

Biological Process

maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
rRNA processing

Molecular Function

RNA binding

Cellular Component

cellular_component
nucleoplasm
nucleolus
small-subunit processome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000374617
Coding exons: 15
Length: 10420
Individuals with no LoFs: 125669
Homozygous LoFs: 0
Heterozygous LoFs: 79
Defined: 125748
p: 0.000314

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.861	320	366	0.873	0.0000215	3923
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00037	0.00037	rare
Latino/Admixed American	0.00029	0.00029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00016	0.00016	rare
Finnish	0.000092	0.000092	rare
European (Non-Finnish)	0.00046	0.00044	rare
South Asian	0.00026	0.00026	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Intolerance Scores

LoFtool: 0.900
RVIS EVS: -0.09
RVIS percentile EVS: 46.92

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: N
Indispensability score: 0.0773

Gene Damage Prediction

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