RWDD3
RWD domain containing 3
Basic information
Region (hg38): 1:95234210-95247225
Links
Phenotypes
GenCC
Source:
No genCC data.
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 RWDD3 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 | 12 | 13 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 12 | 1 | 0 |
Variants in RWDD3
This is a list of pathogenic ClinVar variants found in the RWDD3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-95234256-T-G | not specified | Uncertain significance (May 30, 2023) | ||
| 1-95244217-A-G | not specified | Uncertain significance (Sep 29, 2023) | ||
| 1-95244263-T-G | not specified | Uncertain significance (Dec 15, 2023) | ||
| 1-95244274-C-A | not specified | Uncertain significance (Sep 16, 2021) | ||
| 1-95244297-C-T | not specified | Uncertain significance (Sep 13, 2023) | ||
| 1-95244307-A-G | not specified | Uncertain significance (Dec 20, 2023) | ||
| 1-95244331-C-G | not specified | Uncertain significance (Jul 06, 2021) | ||
| 1-95244345-C-A | not specified | Uncertain significance (Feb 15, 2023) | ||
| 1-95244516-A-G | not specified | Uncertain significance (Aug 21, 2023) | ||
| 1-95244528-A-G | not specified | Likely benign (Jun 12, 2023) | ||
| 1-95244576-G-A | not specified | Uncertain significance (Aug 13, 2021) | ||
| 1-95244662-A-G | not specified | Uncertain significance (Mar 25, 2024) | ||
| 1-95246544-G-C | not specified | Uncertain significance (Oct 06, 2021) | ||
| 1-95246633-C-T | not specified | Uncertain significance (Jul 08, 2022) | ||
| 1-95246763-G-A | not specified | Uncertain significance (Mar 28, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RWDD3 | protein_coding | protein_coding | ENST00000370202 | 4 | 13071 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00148 | 0.885 | 124707 | 0 | 87 | 124794 | 0.000349 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.299 | 123 | 133 | 0.927 | 0.00000612 | 1745 |
| Missense in Polyphen | 35 | 38.902 | 0.89971 | 565 | ||
| Synonymous | 0.179 | 50 | 51.6 | 0.968 | 0.00000272 | 494 |
| Loss of Function | 1.38 | 6 | 10.9 | 0.550 | 4.58e-7 | 154 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00286 | 0.00281 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00172 | 0.00156 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000894 | 0.0000883 |
| Middle Eastern | 0.00172 | 0.00156 |
| South Asian | 0.000135 | 0.000131 |
| Other | 0.000165 | 0.000165 |
dbNSFP
Source:
- Function
- FUNCTION: Enhancer of SUMO conjugation. Via its interaction with UBE2I/UBC9, increases SUMO conjugation to proteins by promoting the binding of E1 and E2 enzymes, thioester linkage between SUMO and UBE2I/UBC9 and transfer of SUMO to specific target proteins which include HIF1A, PIAS, NFKBIA, NR3C1 and TOP1. Isoform 1 and isoform 2 positively regulate the NF-kappa-B signaling pathway by enhancing the sumoylation of NF-kappa-B inhibitor alpha (NFKBIA), promoting its stabilization which consequently leads to an increased inhibition of NF-kappa-B transcriptional activity. Isoform 1 and isoform 2 negatively regulate the hypoxia-inducible factor-1 alpha (HIF1A) signaling pathway by increasing the sumoylation of HIF1A, promoting its stabilization, transcriptional activity and the expression of its target gene VEGFA during hypoxia. Isoform 2 promotes the sumoylation and transcriptional activity of the glucocorticoid receptor NR3C1 and enhances the interaction of SUMO1 and NR3C1 with UBE2I/UBC9. Has no effect on ubiquitination. {ECO:0000269|PubMed:17956732, ECO:0000269|PubMed:22009797, ECO:0000269|PubMed:23469069, ECO:0000269|PubMed:23508108}.;
- Pathway
- SUMO is transferred from E1 to E2 (UBE2I, UBC9);Post-translational protein modification;Metabolism of proteins;Processing and activation of SUMO;SUMOylation
(Consensus)
Recessive Scores
- pRec
- 0.0397
Intolerance Scores
- loftool
- 0.785
- rvis_EVS
- 0.35
- rvis_percentile_EVS
- 74.18
Haploinsufficiency Scores
- pHI
- 0.0301
- hipred
- N
- hipred_score
- 0.167
- ghis
- 0.490
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.0433
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rwdd3
- Phenotype
- cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); limbs/digits/tail phenotype;
Gene ontology
- Biological process
- negative regulation of NF-kappaB transcription factor activity;positive regulation of protein sumoylation;positive regulation of hypoxia-inducible factor-1alpha signaling pathway
- Cellular component
- nucleus;cytoplasm
- Molecular function
- protein binding