WDR64

WD repeat domain 64, the group of WD repeat domain containing

Basic information

Region (hg38): 1:241652277-241802777

Links

ENSG00000162843 ∙ NCBI:128025 ∙ ∙ HGNC:26570 ∙ Uniprot:B1ANS9 ∙ 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 WDR64 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WDR64 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			54	1		55
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	54	1	0

Variants in WDR64

This is a list of pathogenic ClinVar variants found in the WDR64 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-241652506-C-T		not specified	Uncertain significance (Nov 17, 2022)
1-241652507-G-C		not specified	Uncertain significance (Aug 12, 2021)
1-241652518-G-A		not specified	Uncertain significance (Jan 20, 2023)
1-241652528-T-A		not specified	Uncertain significance (Dec 02, 2022)
1-241652598-T-G		not specified	Uncertain significance (Apr 29, 2024)
1-241660575-T-C		not specified	Uncertain significance (Dec 28, 2022)
1-241660587-T-G		not specified	Uncertain significance (Oct 25, 2022)
1-241660607-C-G		not specified	Uncertain significance (May 14, 2024)
1-241660608-G-A		not specified	Uncertain significance (Feb 28, 2024)
1-241660620-A-G		not specified	Uncertain significance (Jul 21, 2021)
1-241660637-G-A		not specified	Uncertain significance (Aug 02, 2021)
1-241671162-G-A		not specified	Uncertain significance (Sep 27, 2021)
1-241674652-A-G		not specified	Uncertain significance (Jul 19, 2023)
1-241674733-G-C		not specified	Uncertain significance (Jun 10, 2022)
1-241679557-A-C		not specified	Uncertain significance (Dec 27, 2022)
1-241679569-G-C		not specified	Uncertain significance (Dec 27, 2023)
1-241683500-T-C		not specified	Uncertain significance (Oct 26, 2022)
1-241683520-T-G		not specified	Uncertain significance (May 27, 2022)
1-241683544-C-T		not specified	Likely benign (Jan 26, 2023)
1-241683660-A-C		not specified	Uncertain significance (Oct 13, 2023)
1-241683689-A-C		not specified	Uncertain significance (Jan 12, 2024)
1-241687481-A-G		not specified	Uncertain significance (Nov 07, 2022)
1-241687501-A-G		not specified	Uncertain significance (Apr 25, 2022)
1-241687565-T-G		not specified	Uncertain significance (Nov 18, 2023)
1-241711867-T-C		not specified	Uncertain significance (Sep 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WDR64	protein_coding	protein_coding	ENST00000366552	27	149856

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.96e-32	0.000872	125415	1	332	125748	0.00133

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.864	500	557	0.897	0.0000285	7156
Missense in Polyphen		143	165.86	0.86217		2124
Synonymous	0.532	186	195	0.952	0.0000101	1969
Loss of Function	0.988	53	61.3	0.864	0.00000347	741

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00587	0.00586
Ashkenazi Jewish	0.00268	0.00268
East Asian	0.000926	0.000925
Finnish	0.000142	0.000139
European (Non-Finnish)	0.000435	0.000422
Middle Eastern	0.000926	0.000925
South Asian	0.00173	0.00163
Other	0.00181	0.00179

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• pHI: 0.236
• hipred: N
• hipred_score: 0.169

Essentials

• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.126

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Wdr64