WDR82
protein-codingWD repeat domain 82, the group of WD repeat domain containing|MicroRNA protein coding host genes
Gene summary
TMEM113 (WDR82) is a component of the mammalian SET1A (MIM 611052)/SET1B (MIM 611055) histone H3-Lys4 methyltransferase complexes (Lee and Skalnik, 2005 [PubMed 16253997]; Lee et al., 2007 [PubMed 17355966]).[supplied by OMIM, Jul 2010]
- TMEM113
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~33.6 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to WDR82 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_025222.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | 2 | |||
| missense | 14 | 14 | ||||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 5 | 5 | ||||
| Total | 0 | 0 | 22 | 1 | 0 | 23 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_079498.2 | 9 | MANE Select | |
| Ensembl | ENSP00000296490.3 | 9 | MANE Select | |
| Ensembl | ENSP00000417313.2 | 6 | Standard | |
| Ensembl | ENSP00000417313.2 | 6 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| wdr82 | Danio rerio | Structure: pharyngeal arch 1 Quality: decreased size abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- mRNA surveillance pathway - Homo sapiens (human)
- miR-targeted genes in epithelium - TarBase
- miR-targeted genes in lymphocytes - TarBase
- miR-targeted genes in muscle cell - TarBase
Biological Process
- histone H3-K4 methylation
- histone H3-K4 trimethylation
Molecular Function
- chromatin binding
- protein binding
- histone methyltransferase activity (H3-K4 specific)
Cellular Component
- nuclear chromosome, telomeric region
- chromatin
- nucleolus
- histone methyltransferase complex
- Set1C/COMPASS complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000296490
- Coding exons
- 9
- Length
- 33600
- Individuals with no LoFs
- 123899
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 2
- Defined
- 123901
- p
- 0.00000807
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 3.29 | 55 | 179 | 0.307 | 0.00000884 | 2096 |
| Missense (PolyPhen) | 3 | 42.026 | 0.071385 | 501 | ||
| Synonymous | 0.948 | 53 | 62.5 | 0.847 | 0.00000315 | 564 |
| Loss of Function | 3.23 | 2 | 15.9 | 0.126 | 8.03e-7 | 194 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000018 | 0.000018 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Regulatory component of the SET1 complex implicated in the tethering of this complex to transcriptional start sites of active genes. Facilitates histone H3 'Lys-4' methylation via recruitment of the SETD1A or SETD1B to the 'Ser-5' phosphorylated C-terminal domain (CTD) of RNA polymerase II large subunit (POLR2A). Component of PTW/PP1 phosphatase complex, which plays a role in the control of chromatin structure and cell cycle progression during the transition from mitosis into interphase. {ECO:0000269|PubMed:17998332, ECO:0000269|PubMed:18838538, ECO:0000269|PubMed:20516061}.;
Recessive Scores
- pRec
- 0.130
Intolerance Scores
- LoFtool
- 0.108
- RVIS EVS
- -0.03
- RVIS percentile EVS
- 51.04
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- E
- Essential (gene trap)
- E
- Indispensability pred.
- E
- Indispensability score
- 0.902
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Low | Low | Low |
| Primary Immunodeficiency | Low | Low | Low |
| Cancer | Low | Low | Low |