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
Phenotypes
GenCC
Source:
- neurodevelopmental disorder (Moderate), mode of inheritance: AD
ClinVar
This is a list of variants' phenotypes submitted to
- not_provided (19 variants)
- not_specified (14 variants)
- Neurodevelopmental_disorder (1 variants)
- WDR5-related_neurodevelopmental_delay (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. These statistics are base on transcript: NM_000017588.3. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 3 | |||||
| missense | 27 | 30 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 2 | 1 | 27 | 3 | 0 |
Loading clinvar variants...
GnomAD
Source:
| 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:
- 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
- loftool
- 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
- Phenotype
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)