WDR5

WD repeat domain 5, the group of WD repeat domain containing|WRAD complex|ATAC complex|NSL histone acetyltransferase complex|Cilia and flagella associated

Basic information

Region (hg38): 9:134135365-134159968

Links

ENSG00000196363 ∙ NCBI:11091 ∙ OMIM:609012 ∙ HGNC:12757 ∙ Uniprot:P61964 ∙ 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 WDR5 gene.

• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WDR5 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	1		9			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding			1			1
Total	1	0	10	0	0

Variants in WDR5

This is a list of pathogenic ClinVar variants found in the WDR5 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-134139882-C-T		not specified	Uncertain significance (Sep 29, 2023)
9-134139896-A-C			not provided (-)
9-134139910-G-T		not specified	Uncertain significance (Dec 02, 2022)
9-134139942-C-G		not specified	Uncertain significance (Jul 14, 2021)
9-134140716-A-G		not specified	Uncertain significance (Nov 11, 2024)
9-134140728-C-T		not specified	Uncertain significance (Feb 15, 2024)
9-134140796-T-C		WDR5-related neurodevelopmental delay	Likely pathogenic (Oct 07, 2024)
9-134141539-G-A		not specified	Uncertain significance (Sep 16, 2021)
9-134141552-A-T		not specified	Uncertain significance (Apr 25, 2023)
9-134142039-G-GT		Neurodevelopmental disorder	Uncertain significance (Mar 12, 2024)
9-134142369-T-G			Uncertain significance (Feb 08, 2024)
9-134142670-C-T			Uncertain significance (Nov 01, 2023)
9-134142686-G-T			Uncertain significance (Jul 02, 2024)
9-134142703-C-T			Uncertain significance (Feb 22, 2022)
9-134142715-C-T			Uncertain significance (Apr 11, 2024)
9-134151984-C-T			Pathogenic (Feb 13, 2024)
9-134152021-C-T			Pathogenic (Feb 01, 2024)
9-134154486-T-G		not specified	Uncertain significance (Jul 27, 2021)
9-134154511-G-A			Uncertain significance (Jan 12, 2024)
9-134154514-A-G			Uncertain significance (Feb 08, 2024)
9-134157962-A-G			Uncertain significance (Oct 13, 2022)
9-134157967-A-G			Uncertain significance (May 22, 2023)
9-134159934-TTC-T		Congenital heart disease	Uncertain significance (Jul 23, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WDR5	protein_coding	protein_coding	ENST00000358625	13	24607

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000222	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.39	63	197	0.320	0.0000115	2180
Missense in Polyphen		7	69.676	0.10047		796
Synonymous	0.257	82	85.0	0.965	0.00000615	624
Loss of Function	4.54	0	24.0	0.00	0.00000122	269

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: Contributes to histone modification. May position the N- terminus of histone H3 for efficient trimethylation at 'Lys-4'. As part of the MLL1/MLL complex it is involved in methylation and dimethylation at 'Lys-4' of histone H3. H3 'Lys-4' methylation represents a specific tag for epigenetic transcriptional activation. As part of the NSL complex it may be involved in acetylation of nucleosomal histone H4 on several lysine residues. May regulate osteoblasts differentiation. {ECO:0000269|PubMed:16600877, ECO:0000269|PubMed:16829960, ECO:0000269|PubMed:19103755, ECO:0000269|PubMed:19556245, ECO:0000269|PubMed:20018852}.
• Pathway: Cushing,s syndrome - Homo sapiens (human);Gene expression (Transcription);Generic Transcription Pathway;Post-translational protein modification;Metabolism of proteins;PKMTs methylate histone lysines;RNA Polymerase II Transcription;RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function;RMTs methylate histone arginines;Chromatin modifying enzymes;HATs acetylate histones;Neddylation;Chromatin organization;Circadian rhythm pathway;Transcriptional regulation by RUNX1 (Consensus)

Recessive Scores

• pRec: 0.178

Intolerance Scores

• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.42

Haploinsufficiency Scores

• pHI: 0.368
• hipred: Y
• hipred_score: 0.841
• ghis: 0.691

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.553

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Wdr5

Gene ontology

• Biological process: skeletal system development;neuron projection development;positive regulation of gluconeogenesis by positive regulation of transcription from RNA polymerase II promoter;post-translational protein modification;histone H3 acetylation;histone H4-K5 acetylation;histone H4-K8 acetylation;histone H4-K16 acetylation;regulation of megakaryocyte differentiation;histone H3-K4 methylation
• Cellular component: histone acetyltransferase complex;nucleus;nucleoplasm;Ada2/Gcn5/Ada3 transcription activator complex;histone methyltransferase complex;MLL3/4 complex;Set1C/COMPASS complex;MLL1 complex
• Molecular function: protein binding;histone-lysine N-methyltransferase activity;methylated histone binding;histone binding;histone methyltransferase activity (H3-K4 specific);histone acetyltransferase activity (H4-K5 specific);histone acetyltransferase activity (H4-K8 specific);histone acetyltransferase activity (H4-K16 specific)