WDR54

WD repeat domain 54, the group of WD repeat domain containing

Basic information

Region (hg38): 2:74421678-74425755

Links

ENSG00000005448 ∙ NCBI:84058 ∙ ∙ HGNC:25770 ∙ Uniprot:Q9H977 ∙ 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 WDR54 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WDR54 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				1		1
missense			28	2		30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	3	0

Variants in WDR54

This is a list of pathogenic ClinVar variants found in the WDR54 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-74422163-T-C		not specified	Likely benign (Feb 03, 2022)
2-74422175-A-T		not specified	Uncertain significance (Aug 08, 2023)
2-74422185-G-C		not specified	Uncertain significance (Apr 11, 2023)
2-74422191-C-T		not specified	Uncertain significance (Mar 11, 2024)
2-74422238-C-T		not specified	Uncertain significance (Dec 18, 2023)
2-74422276-C-A		not specified	Uncertain significance (Dec 20, 2023)
2-74422344-G-T		not specified	Uncertain significance (Jun 23, 2023)
2-74422355-A-C		not specified	Uncertain significance (Sep 25, 2023)
2-74422916-C-T		not specified	Uncertain significance (Apr 25, 2022)
2-74423332-A-G		not specified	Uncertain significance (May 26, 2023)
2-74423862-G-C		not specified	Uncertain significance (May 29, 2024)
2-74423869-C-T		not specified	Uncertain significance (Dec 08, 2023)
2-74423870-G-A		not specified	Uncertain significance (Apr 04, 2023)
2-74423881-T-C		not specified	Uncertain significance (May 18, 2022)
2-74423924-A-G		not specified	Uncertain significance (Feb 15, 2023)
2-74423938-C-G		not specified	Uncertain significance (Oct 12, 2021)
2-74423940-G-T		not specified	Uncertain significance (Feb 17, 2022)
2-74423963-C-T		not specified	Uncertain significance (Dec 26, 2023)
2-74423967-G-A			Likely benign (Jun 01, 2020)
2-74423971-G-A		not specified	Uncertain significance (Sep 28, 2022)
2-74424879-G-T		not specified	Uncertain significance (Nov 09, 2021)
2-74424930-G-A		not specified	Uncertain significance (May 26, 2022)
2-74424948-C-T		not specified	Uncertain significance (May 30, 2023)
2-74424960-G-A		not specified	Uncertain significance (Oct 27, 2022)
2-74424974-G-C		not specified	Uncertain significance (Jul 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WDR54	protein_coding	protein_coding	ENST00000348227	9	4078

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.57e-11	0.108	125701	0	47	125748	0.000187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.441	178	195	0.911	0.0000105	2129
Missense in Polyphen		34	47.363	0.71786		522
Synonymous	-1.11	93	80.4	1.16	0.00000444	713
Loss of Function	0.483	18	20.4	0.884	0.00000109	196

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000210	0.000210
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000273	0.000273
Middle Eastern	0.000109	0.000109
South Asian	0.000229	0.000229
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.472
• rvis_EVS: 0.2
• rvis_percentile_EVS: 67.19

Haploinsufficiency Scores

• pHI: 0.150
• hipred: N
• hipred_score: 0.248
• ghis: 0.510

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0652

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Wdr54