WDR5B

WD repeat domain 5B, the group of WD repeat domain containing

Basic information

Region (hg38): 3:122411846-122416062

Links

ENSG00000196981 ∙ NCBI:54554 ∙ ∙ HGNC:17826 ∙ Uniprot:Q86VZ2 ∙ 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 WDR5B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WDR5B 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			16	1		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	1	0

Variants in WDR5B

This is a list of pathogenic ClinVar variants found in the WDR5B region.

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

Position	Type	Phenotype	Significance	ClinVar
3-122414567-T-G		not specified	Uncertain significance (Sep 18, 2024)
3-122414732-C-T		not specified	Uncertain significance (Oct 16, 2024)
3-122414733-C-T		not specified	Uncertain significance (Oct 14, 2023)
3-122414778-G-A		not specified	Uncertain significance (Oct 08, 2024)
3-122414781-C-T		not specified	Uncertain significance (Oct 26, 2022)
3-122414810-C-G		not specified	Uncertain significance (Oct 01, 2024)
3-122414824-T-A		not specified	Uncertain significance (Dec 15, 2023)
3-122414877-A-T		not specified	Uncertain significance (Aug 21, 2024)
3-122414880-T-G		not specified	Uncertain significance (Jul 16, 2024)
3-122414891-A-C		not specified	Uncertain significance (Feb 28, 2023)
3-122414902-A-C		not specified	Uncertain significance (Feb 28, 2023)
3-122414907-C-T		not specified	Uncertain significance (Aug 17, 2022)
3-122415026-T-C		not specified	Uncertain significance (May 23, 2023)
3-122415111-T-C		not specified	Uncertain significance (Nov 24, 2024)
3-122415125-G-A		not specified	Uncertain significance (Jan 23, 2024)
3-122415158-T-A		not specified	Uncertain significance (Jan 31, 2024)
3-122415161-C-T		not specified	Uncertain significance (Aug 02, 2024)
3-122415188-G-T		not specified	Uncertain significance (Aug 13, 2021)
3-122415198-C-A		not specified	Uncertain significance (Jun 29, 2023)
3-122415357-T-C		not specified	Uncertain significance (Nov 03, 2022)
3-122415360-C-T		not specified	Uncertain significance (Nov 09, 2024)
3-122415428-T-C		not specified	Likely benign (Mar 16, 2022)
3-122415428-T-G		not specified	Uncertain significance (Dec 19, 2023)
3-122415486-G-T		not specified	Uncertain significance (Jul 05, 2023)
3-122415491-A-G		not specified	Likely benign (Jun 05, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WDR5B	protein_coding	protein_coding	ENST00000330689	1	4168

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000180	0.464	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.450	183	167	1.10	0.00000807	2143
Missense in Polyphen		55	53.043	1.0369		680
Synonymous	-0.504	73	67.7	1.08	0.00000367	653
Loss of Function	0.497	8	9.67	0.828	4.17e-7	145

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May function as a substrate receptor for CUL4-DDB1 ubiquitin E3 ligase complex. {ECO:0000250}.
• Pathway: Cushing,s syndrome - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.691
• rvis_EVS: 0.11
• rvis_percentile_EVS: 61.73

Haploinsufficiency Scores

• pHI: 0.401
• hipred: N
• hipred_score: 0.310

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.515

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Wdr5b

Gene ontology

• Biological process: histone H3-K4 methylation
• Cellular component: nucleus;Set1C/COMPASS complex
• Molecular function: histone binding