WDR25

WD repeat domain 25, the group of WD repeat domain containing

Basic information

Region (hg38): 14:100376417-100530303

Previous symbols: [ "C14orf67" ]

Links

ENSG00000176473 ∙ NCBI:79446 ∙ OMIM:618059 ∙ HGNC:21064 ∙ Uniprot:Q64LD2 ∙ 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 WDR25 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WDR25 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			29	3		32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	3	0

Variants in WDR25

This is a list of pathogenic ClinVar variants found in the WDR25 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-100380937-A-G		not specified	Uncertain significance (Jun 24, 2022)
14-100380944-C-A		not specified	Uncertain significance (Nov 17, 2023)
14-100381001-A-G		not specified	Uncertain significance (Jul 27, 2021)
14-100381006-G-A		not specified	Uncertain significance (Aug 08, 2023)
14-100381037-A-G		not specified	Uncertain significance (May 31, 2023)
14-100381058-C-T		not specified	Uncertain significance (May 10, 2024)
14-100381064-G-A		not specified	Likely benign (Dec 09, 2023)
14-100381076-C-T		not specified	Uncertain significance (Mar 27, 2023)
14-100381222-G-A		not specified	Likely benign (Feb 27, 2023)
14-100381244-T-C		not specified	Uncertain significance (Feb 21, 2024)
14-100381255-G-C		not specified	Uncertain significance (Mar 26, 2024)
14-100381345-A-G		not specified	Uncertain significance (May 11, 2022)
14-100381451-A-G		not specified	Uncertain significance (Feb 06, 2023)
14-100381462-A-G		not specified	Uncertain significance (May 04, 2023)
14-100381513-G-T		not specified	Uncertain significance (Feb 06, 2023)
14-100381547-C-G		not specified	Uncertain significance (Sep 26, 2022)
14-100381561-G-A		not specified	Uncertain significance (Feb 16, 2023)
14-100381592-C-T		not specified	Uncertain significance (Sep 28, 2023)
14-100381627-C-A		not specified	Uncertain significance (Jun 28, 2022)
14-100381729-A-G		not specified	Uncertain significance (May 25, 2022)
14-100468021-G-T		not specified	Uncertain significance (Apr 13, 2022)
14-100468038-C-A		Long QT syndrome	Likely benign (-)
14-100468040-C-G		not specified	Uncertain significance (Jul 25, 2023)
14-100468073-C-G		not specified	Uncertain significance (Mar 25, 2024)
14-100468093-C-T		not specified	Uncertain significance (Nov 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WDR25	protein_coding	protein_coding	ENST00000335290	6	153886

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000214	0.979	125690	0	58	125748	0.000231

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.637	299	332	0.901	0.0000202	3529
Missense in Polyphen		96	125.59	0.76441		1292
Synonymous	0.489	129	136	0.947	0.00000858	1127
Loss of Function	2.08	11	21.4	0.515	0.00000116	232

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000796	0.000795
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000230	0.000229
Middle Eastern	0.000163	0.000163
South Asian	0.0000981	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0955

Intolerance Scores

• loftool: 0.718
• rvis_EVS: 0.27
• rvis_percentile_EVS: 70.69

Haploinsufficiency Scores

• pHI: 0.172
• hipred: N
• hipred_score: 0.331
• ghis: 0.396

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.963

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Wdr25

Gene ontology

• Molecular function: protein binding