WDR55

WD repeat domain 55, the group of WD repeat domain containing

Basic information

Region (hg38): 5:140664868-140674124

Links

ENSG00000120314 ∙ NCBI:54853 ∙ ∙ HGNC:25971 ∙ Uniprot:Q9H6Y2 ∙ 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 WDR55 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WDR55 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			22	1		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			9			9
Total	0	0	31	1	0

Variants in WDR55

This is a list of pathogenic ClinVar variants found in the WDR55 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-140664986-C-T		not specified	Uncertain significance (Sep 22, 2023)
5-140664998-G-A		not specified	Uncertain significance (Oct 01, 2024)
5-140665004-C-T		not specified	Uncertain significance (Dec 07, 2024)
5-140665007-C-T		not specified	Uncertain significance (Oct 07, 2024)
5-140665037-G-A		not specified	Uncertain significance (Sep 12, 2023)
5-140668242-A-G		not specified	Uncertain significance (Feb 17, 2022)
5-140668251-A-C		not specified	Uncertain significance (Dec 14, 2021)
5-140668269-A-C		not specified	Uncertain significance (May 05, 2023)
5-140668305-G-A		not specified	Uncertain significance (Apr 20, 2023)
5-140668484-G-A		not specified	Uncertain significance (May 30, 2023)
5-140668673-G-A		not specified	Uncertain significance (Feb 22, 2024)
5-140668679-A-G		not specified	Likely benign (Mar 17, 2023)
5-140668721-A-G		not specified	Uncertain significance (Oct 21, 2024)
5-140668724-A-T		not specified	Uncertain significance (Mar 01, 2023)
5-140668742-A-G		not specified	Uncertain significance (Nov 21, 2024)
5-140668923-A-G		not specified	Uncertain significance (Jun 30, 2023)
5-140668928-C-T		not specified	Uncertain significance (Apr 09, 2024)
5-140668936-T-A		not specified	Uncertain significance (Aug 14, 2024)
5-140668961-G-T		not specified	Uncertain significance (Feb 23, 2023)
5-140669079-T-G		not specified	Uncertain significance (Dec 10, 2024)
5-140669161-G-A		not specified	Uncertain significance (Feb 27, 2023)
5-140669230-C-A		not specified	Uncertain significance (Aug 04, 2024)
5-140669236-A-C		not specified	Uncertain significance (Jan 19, 2024)
5-140669239-G-C		not specified	Uncertain significance (Dec 03, 2024)
5-140669350-C-T		not specified	Uncertain significance (Aug 10, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WDR55	protein_coding	protein_coding	ENST00000358337	7	9449

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.04e-14	0.00738	125634	0	114	125748	0.000453

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.972	186	227	0.819	0.0000125	2500
Missense in Polyphen		54	74.454	0.72528		816
Synonymous	0.973	73	84.4	0.865	0.00000419	783
Loss of Function	-0.550	19	16.6	1.15	9.60e-7	172

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000792	0.000791
Ashkenazi Jewish	0.000696	0.000695
East Asian	0.0000544	0.0000544
Finnish	0.0000946	0.0000924
European (Non-Finnish)	0.000550	0.000545
Middle Eastern	0.0000544	0.0000544
South Asian	0.000393	0.000392
Other	0.000652	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Nucleolar protein that acts as a modulator of rRNA synthesis. Plays a central role during organogenesis (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.108

Intolerance Scores

• rvis_EVS: 0.46
• rvis_percentile_EVS: 78.59

Haploinsufficiency Scores

• pHI: 0.0387
• hipred: N
• hipred_score: 0.282
• ghis: 0.533

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.234

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Wdr55
• 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)

Zebrafish Information Network

• Gene name: wdr55
• Affected structure: anatomical system
• Phenotype tag: abnormal
• Phenotype quality: quality

Gene ontology

• Biological process: rRNA processing;biological_process
• Cellular component: cellular_component;nucleolus;cytoplasm
• Molecular function: molecular_function