WDR3

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

Basic information

Region (hg38): 1:117929720-117966543

Links

ENSG00000065183 ∙ NCBI:10885 ∙ OMIM:604737 ∙ HGNC:12755 ∙ Uniprot:Q9UNX4 ∙ 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 WDR3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WDR3 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			47	1		48
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			4	1		5
Total	0	0	51	2	0

Variants in WDR3

This is a list of pathogenic ClinVar variants found in the WDR3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-117933344-C-T		not specified	Uncertain significance (Aug 02, 2021)
1-117933356-A-T		not specified	Uncertain significance (Jan 04, 2022)
1-117933381-G-C		not specified	Uncertain significance (May 23, 2023)
1-117933392-A-G		not specified	Uncertain significance (Jun 27, 2022)
1-117933414-G-T		not specified	Uncertain significance (May 11, 2022)
1-117933419-G-C		not specified	Uncertain significance (Feb 03, 2022)
1-117933429-G-A		not specified	Uncertain significance (Oct 29, 2021)
1-117933447-C-G		not specified	Uncertain significance (Dec 16, 2023)
1-117934489-G-T		not specified	Uncertain significance (Jun 18, 2021)
1-117934552-A-G		not specified	Uncertain significance (Mar 19, 2024)
1-117934614-G-A		not specified	Uncertain significance (Sep 12, 2023)
1-117934657-G-T		not specified	Uncertain significance (Jun 28, 2023)
1-117936818-G-A		not specified	Uncertain significance (Dec 06, 2022)
1-117936868-A-G		not specified	Uncertain significance (Jun 11, 2021)
1-117938511-C-G		not specified	Uncertain significance (May 07, 2024)
1-117938523-C-A		not specified	Uncertain significance (Jun 03, 2022)
1-117940873-C-T		not specified	Uncertain significance (Dec 15, 2022)
1-117941125-G-A		not specified	Uncertain significance (Jun 05, 2023)
1-117941161-G-A		not specified	Uncertain significance (Jul 14, 2021)
1-117942511-G-A		not specified	Uncertain significance (Jan 04, 2022)
1-117942524-A-G		not specified	Uncertain significance (Oct 13, 2023)
1-117942528-A-G		not specified	Uncertain significance (Jan 02, 2024)
1-117943530-T-C		not specified	Uncertain significance (Jun 02, 2023)
1-117943541-C-T		not specified	Uncertain significance (Dec 07, 2021)
1-117943589-C-G		not specified	Uncertain significance (Jun 28, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WDR3	protein_coding	protein_coding	ENST00000349139	26	36823

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.10e-13	1.00	125536	0	212	125748	0.000843

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.600	463	501	0.925	0.0000254	6185
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000996	0.000993
Ashkenazi Jewish	0.00101	0.000993
East Asian	0.000872	0.000870
Finnish	0.00192	0.00180
European (Non-Finnish)	0.000746	0.000730
Middle Eastern	0.000872	0.000870
South Asian	0.00118	0.00118
Other	0.000824	0.000815

dbNSFP

Source: dbNSFP

• Pathway: 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 (Consensus)

Recessive Scores

• pRec: 0.114

Intolerance Scores

• loftool: 0.815
• rvis_EVS: -0.19
• rvis_percentile_EVS: 39.24

Haploinsufficiency Scores

• pHI: 0.750
• hipred: Y
• hipred_score: 0.672
• ghis: 0.597

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.793

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Wdr3
• 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)

Gene ontology

• Biological process: rRNA processing
• Cellular component: nucleus;nucleoplasm;nucleolus;nuclear membrane;small-subunit processome;Pwp2p-containing subcomplex of 90S preribosome
• Molecular function: RNA binding