RUVBL2
RuvB like AAA ATPase 2, the group of SRCAP complex|INO80 complex |DNA helicases|R2SP complex|MicroRNA protein coding host genes|Tip60/Nua4 histone acetyltransferase complex subunits|AAA ATPases|R2TP complex
Basic information
Region (hg38): 19:48993561-49015970
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn genetic diseases (14 variants)
- not provided (6 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the RUVBL2 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 | 4 | |||||
| missense | 14 | 14 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region ? | 1 | 1 | ||||
| non coding ? | 1 | |||||
| Total | 0 | 0 | 14 | 1 | 4 |
Variants in RUVBL2
This is a list of pathogenic ClinVar variants found in the RUVBL2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 19-48999338-C-T | not specified | Uncertain significance (Sep 13, 2023) | ||
| 19-48999347-G-A | not specified | Uncertain significance (Aug 21, 2023) | ||
| 19-49003317-G-A | not specified | Uncertain significance (Sep 01, 2021) | ||
| 19-49004325-G-A | not specified | Uncertain significance (Dec 12, 2023) | ||
| 19-49007059-A-G | not specified | Uncertain significance (Dec 28, 2022) | ||
| 19-49007141-G-A | not specified | Uncertain significance (Sep 01, 2021) | ||
| 19-49007357-G-A | not specified | Uncertain significance (Dec 21, 2023) | ||
| 19-49007358-C-A | not specified | Uncertain significance (Dec 01, 2022) | ||
| 19-49009880-C-T | Benign (Jul 17, 2018) | |||
| 19-49010042-C-T | Benign (May 08, 2018) | |||
| 19-49010048-C-T | Likely benign (Dec 01, 2022) | |||
| 19-49010528-G-A | not specified | Uncertain significance (Oct 29, 2021) | ||
| 19-49010582-G-A | not specified | Uncertain significance (Mar 14, 2023) | ||
| 19-49011025-G-A | not specified | Uncertain significance (Nov 22, 2023) | ||
| 19-49011063-C-T | Benign (Jul 16, 2018) | |||
| 19-49011284-C-G | not specified | Uncertain significance (Aug 30, 2022) | ||
| 19-49014569-A-T | not specified | Uncertain significance (Feb 23, 2023) | ||
| 19-49014596-C-T | not specified | Uncertain significance (Feb 22, 2023) | ||
| 19-49015097-C-T | not specified | Uncertain significance (Mar 21, 2022) | ||
| 19-49015102-C-T | Benign (Jun 28, 2018) | |||
| 19-49015139-C-T | not specified | Uncertain significance (Oct 26, 2022) | ||
| 19-49015801-T-C | Benign (Aug 09, 2018) | |||
| 19-49015822-G-A | not specified | Uncertain significance (Jul 20, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RUVBL2 | protein_coding | protein_coding | ENST00000595090 | 15 | 22548 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 0.0000800 | 124734 | 0 | 2 | 124736 | 0.00000802 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.11 | 178 | 339 | 0.524 | 0.0000244 | 2989 |
| Missense in Polyphen | 51 | 156.46 | 0.32596 | 1287 | ||
| Synonymous | 0.0441 | 139 | 140 | 0.995 | 0.0000105 | 928 |
| Loss of Function | 4.79 | 0 | 26.8 | 0.00 | 0.00000137 | 288 |
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) | 0.0000102 | 0.00000883 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000328 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Possesses single-stranded DNA-stimulated ATPase and ATP- dependent DNA helicase (5' to 3') activity; hexamerization is thought to be critical for ATP hydrolysis and adjacent subunits in the ring-like structure contribute to the ATPase activity.; FUNCTION: Proposed core component of the chromatin remodeling INO80 complex which is involved in transcriptional regulation, DNA replication and probably DNA repair.; FUNCTION: Involved in the endoplasmic reticulum (ER)-associated degradation (ERAD) pathway where it negatively regulates expression of ER stress response genes. {ECO:0000269|PubMed:25652260}.;
- Pathway
- Chromatin modifying enzymes;ATF-2 transcription factor network;HATs acetylate histones;Telomere Extension By Telomerase;Extension of Telomeres;Telomere Maintenance;Chromosome Maintenance;Chromatin organization;C-MYC pathway;Cell Cycle;Integrin-linked kinase signaling;Regulation of nuclear beta catenin signaling and target gene transcription;Validated targets of C-MYC transcriptional activation
(Consensus)
Recessive Scores
- pRec
- 0.546
Intolerance Scores
- loftool
- 0.154
- rvis_EVS
- -1.02
- rvis_percentile_EVS
- 7.94
Haploinsufficiency Scores
- pHI
- 0.610
- hipred
- Y
- hipred_score
- 0.831
- ghis
- 0.673
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.992
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ruvbl2
- Phenotype
- immune system 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); hematopoietic system phenotype; pigmentation phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); endocrine/exocrine gland phenotype;
Zebrafish Information Network
- Gene name
- ruvbl2
- Affected structure
- cardiac muscle cell
- Phenotype tag
- abnormal
- Phenotype quality
- increased amount
Gene ontology
- Biological process
- box C/D snoRNP assembly;DNA repair;DNA recombination;chromatin remodeling;regulation of transcription by RNA polymerase II;protein folding;histone acetylation;DNA duplex unwinding;cellular response to UV;positive regulation of histone acetylation;regulation of growth;histone H4 acetylation;histone H2A acetylation;positive regulation of transcription by RNA polymerase II;establishment of protein localization to chromatin;cellular response to estradiol stimulus;transcriptional activation by promoter-enhancer looping;negative regulation of estrogen receptor binding;negative regulation of canonical Wnt signaling pathway;negative regulation of nucleic acid-templated transcription;positive regulation of telomerase RNA localization to Cajal body
- Cellular component
- Swr1 complex;nucleus;nucleoplasm;nuclear euchromatin;centrosome;cytosol;membrane;nuclear matrix;Ino80 complex;NuA4 histone acetyltransferase complex;extracellular exosome;MLL1 complex;R2TP complex;ribonucleoprotein complex
- Molecular function
- RNA polymerase II core promoter sequence-specific DNA binding;RNA polymerase II distal enhancer sequence-specific DNA binding;TFIID-class transcription factor complex binding;DNA helicase activity;transcription corepressor activity;ATP-dependent DNA helicase activity;protein binding;ATP binding;beta-catenin binding;ATPase activity;TBP-class protein binding;chromatin DNA binding;identical protein binding;protein homodimerization activity;ATP-dependent 5'-3' DNA helicase activity;ADP binding;unfolded protein binding;ATPase binding