WDR3

protein-coding

WD repeat domain 3, the group of WD repeat domain containing|UTPb subcomplex

Gene summary

This gene encodes a nuclear protein containing 10 WD repeats. WD repeats are approximately 30- to 40-amino acid domains containing several conserved residues, which usually include a trp-asp at the C-terminal end. Proteins belonging to the WD repeat family are involved in a variety of cellular processes, including cell cycle progression, signal transduction, apoptosis, and gene regulation. [provided by RefSeq, Jul 2008]

MANE transcript

NM_006784.3

Inheritance

—

ClinVar variants

U:155B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.54

Max pathogenic AF

—

Genomic locus

chr1:117,929,720-117,966,543

External References & Databases

Ensembl (ENSG00000065183)

Transcript & Mutation Effects

hg38 • Region Span ~36.8 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 WDR3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 143

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006784.3. 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			1 clinvar	1 clinvar		2
missense			144 clinvar	4 clinvar		148
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			10 clinvar			10
Total	0	0	155	5	0	160

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 17 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_006784.3	RefSeq	NP_006775.1	26	MANE Select
ENST00000349139.6	Ensembl	ENSP00000308179.4	26	MANE Select
ENST00000369441.7	Ensembl	ENSP00000358449.3	2	Standard
ENST00000880604.1	Ensembl	ENSP00000550663.1	26	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Ribosome biogenesis in eukaryotes - Homo sapiens (human)
rRNA processing
Metabolism of RNA
rRNA modification in the nucleus and cytosol
rRNA processing in the nucleus and cytosol

Biological Process

rRNA processing

Molecular Function

RNA binding

Cellular Component

nucleus
nucleoplasm
nucleolus
nuclear membrane
small-subunit processome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000349139
Coding exons: 26
Length: 36823
Individuals with no LoFs: 125536
Homozygous LoFs: 0
Heterozygous LoFs: 212
Defined: 125748
p: 0.000843

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.600	463	501	0.925	0.0000254	6185
Missense (PolyPhen)		145	165.67	0.87525		1987
Synonymous	-0.389	184	177	1.04	0.00000900	1774
Loss of Function	3.20	30	55.8	0.538	0.00000290	663

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00062	0.00062	rare
Latino/Admixed American	0.00038	0.00038	rare
Ashkenazi Jewish	0.0010	0.00099	notable
East Asian	0.00087	0.00087	rare
Finnish	0.0019	0.0018	notable
European (Non-Finnish)	0.00075	0.00073	rare
South Asian	0.0012	0.0012	notable
Other	0.00082	0.00081	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.114

Intolerance Scores

LoFtool: 0.815
RVIS EVS: -0.19
RVIS percentile EVS: 39.24

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.793

Gene Damage Prediction

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