WTAP
Basic information
Region (hg38): 6:159725585-159756319
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the WTAP 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 | 7 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 7 | 0 | 0 |
Variants in WTAP
This is a list of pathogenic ClinVar variants found in the WTAP region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 6-159748228-G-C | not specified | Uncertain significance (May 27, 2022) | ||
| 6-159748284-A-G | not specified | Uncertain significance (Apr 09, 2024) | ||
| 6-159748286-A-T | not specified | Uncertain significance (Apr 22, 2022) | ||
| 6-159755210-G-A | not specified | Uncertain significance (Dec 27, 2022) | ||
| 6-159755211-A-G | not specified | Uncertain significance (Dec 27, 2022) | ||
| 6-159755213-G-A | not specified | Uncertain significance (May 06, 2022) | ||
| 6-159755270-C-T | not specified | Uncertain significance (Apr 08, 2022) | ||
| 6-159755280-C-T | not specified | Uncertain significance (Nov 18, 2022) | ||
| 6-159755507-C-G | not specified | Uncertain significance (Jun 04, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| WTAP | protein_coding | protein_coding | ENST00000358372 | 7 | 30735 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 0.000335 | 125740 | 0 | 8 | 125748 | 0.0000318 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.27 | 121 | 215 | 0.564 | 0.0000114 | 2612 |
| Missense in Polyphen | 24 | 49.169 | 0.48811 | 681 | ||
| Synonymous | -0.581 | 88 | 81.3 | 1.08 | 0.00000462 | 733 |
| Loss of Function | 4.44 | 0 | 22.9 | 0.00 | 0.00000126 | 236 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000664 | 0.0000664 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000534 | 0.0000527 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Associated component of the WMM complex, a complex that mediates N6-methyladenosine (m6A) methylation of RNAs, a modification that plays a role in the efficiency of mRNA splicing and RNA processing (PubMed:29507755). Required for accumulation of METTL3 and METTL14 to nuclear speckle (PubMed:24316715, PubMed:24407421, PubMed:24981863). Acts as a mRNA splicing regulator (PubMed:12444081). Regulates G2/M cell-cycle transition by binding to the 3' UTR of CCNA2, which enhances its stability (PubMed:17088532). Impairs WT1 DNA-binding ability and inhibits expression of WT1 target genes (PubMed:17095724). {ECO:0000269|PubMed:12444081, ECO:0000269|PubMed:17088532, ECO:0000269|PubMed:17095724, ECO:0000269|PubMed:24316715, ECO:0000269|PubMed:24407421, ECO:0000269|PubMed:24981863, ECO:0000269|PubMed:29507755}.;
- Pathway
- Metabolism of RNA;Processing of Capped Intron-Containing Pre-mRNA
(Consensus)
Recessive Scores
- pRec
- 0.159
Intolerance Scores
- loftool
- 0.345
- rvis_EVS
- -0.14
- rvis_percentile_EVS
- 43.29
Haploinsufficiency Scores
- pHI
- 0.233
- hipred
- Y
- hipred_score
- 0.794
- ghis
- 0.555
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.942
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Wtap
- Phenotype
- embryo phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span);
Zebrafish Information Network
- Gene name
- wtap
- Affected structure
- ventricular system
- Phenotype tag
- abnormal
- Phenotype quality
- decreased size
Gene ontology
- Biological process
- regulation of alternative mRNA splicing, via spliceosome;mRNA processing;cell cycle;multicellular organism development;RNA splicing;mRNA methylation
- Cellular component
- nucleus;nucleoplasm;cytoplasm;nuclear speck;nuclear membrane;RNA N6-methyladenosine methyltransferase complex
- Molecular function
- protein binding