WDR53

WD repeat domain 53, the group of WD repeat domain containing

Basic information

Region (hg38): 3:196554177-196568674

Links

ENSG00000185798 ∙ NCBI:348793 ∙ OMIM:615110 ∙ HGNC:28786 ∙ Uniprot:Q7Z5U6 ∙ 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 WDR53 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WDR53 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			18	4		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	4	0

Variants in WDR53

This is a list of pathogenic ClinVar variants found in the WDR53 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-196554236-G-A		not specified	Uncertain significance (Jul 02, 2024)
3-196554240-T-C		not specified	Uncertain significance (May 18, 2022)
3-196554246-T-C		not specified	Uncertain significance (Oct 17, 2023)
3-196554266-A-G		not specified	Uncertain significance (Jan 04, 2024)
3-196554285-T-C		not specified	Uncertain significance (Oct 01, 2024)
3-196554372-C-A		not specified	Uncertain significance (Nov 24, 2024)
3-196554378-C-T		not specified	Uncertain significance (Nov 11, 2024)
3-196554394-C-G		not specified	Uncertain significance (Oct 06, 2024)
3-196554425-T-C		not specified	Uncertain significance (Aug 04, 2024)
3-196554437-C-T		not specified	Likely benign (Aug 02, 2022)
3-196554473-C-G		not specified	Uncertain significance (Jul 02, 2024)
3-196554491-G-A		not specified	Likely benign (Jan 08, 2024)
3-196554496-C-A		not specified	Uncertain significance (Jul 17, 2024)
3-196554522-G-T		not specified	Uncertain significance (Feb 05, 2024)
3-196554599-T-G		not specified	Uncertain significance (Sep 29, 2022)
3-196554614-C-T		not specified	Uncertain significance (Mar 01, 2023)
3-196554623-C-T		not specified	Uncertain significance (Jun 01, 2023)
3-196554696-C-T		not specified	Uncertain significance (Dec 17, 2023)
3-196554699-G-A		not specified	Uncertain significance (Apr 20, 2023)
3-196554780-G-C		not specified	Uncertain significance (Jun 18, 2024)
3-196561027-T-G		not specified	Uncertain significance (Dec 15, 2023)
3-196561035-C-G		not specified	Uncertain significance (Mar 20, 2024)
3-196561066-T-C		not specified	Uncertain significance (Jun 13, 2023)
3-196561108-A-C		not specified	Uncertain significance (Sep 22, 2023)
3-196561183-T-C		not specified	Uncertain significance (Dec 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WDR53	protein_coding	protein_coding	ENST00000332629	2	14490

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00249	0.936	125670	1	77	125748	0.000310

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.380	174	189	0.922	0.00000981	2328
Missense in Polyphen		37	48.891	0.75679		620
Synonymous	-0.569	82	75.7	1.08	0.00000416	726
Loss of Function	1.64	6	12.2	0.494	6.74e-7	152

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000213	0.000210
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000178	0.000176
Middle Eastern	0.000109	0.000109
South Asian	0.00167	0.00163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.108

Intolerance Scores

• rvis_EVS: -0.18
• rvis_percentile_EVS: 40.16

Haploinsufficiency Scores

• pHI: 0.204
• hipred: N
• hipred_score: 0.204
• ghis: 0.550

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.569

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Wdr53