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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

ENSG00000183207NCBI:10856OMIM:604788HGNC:10475Uniprot:Q9Y230AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RUVBL2 gene.

  • 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
1
clinvar
3
clinvar
4
missense
14
clinvar
14
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
1
1
non coding
1
clinvar
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 Inborn genetic diseases Uncertain significance (Sep 13, 2023)2588243
19-48999347-G-A Inborn genetic diseases Uncertain significance (Aug 21, 2023)2591397
19-49003317-G-A Inborn genetic diseases Uncertain significance (Sep 01, 2021)2206682
19-49007059-A-G Inborn genetic diseases Uncertain significance (Dec 28, 2022)2205750
19-49007141-G-A Inborn genetic diseases Uncertain significance (Sep 01, 2021)2348928
19-49007358-C-A Inborn genetic diseases Uncertain significance (Dec 01, 2022)2330470
19-49009880-C-T Benign (Jul 17, 2018)736300
19-49010042-C-T Benign (May 08, 2018)781514
19-49010048-C-T Likely benign (Dec 01, 2022)2650228
19-49010528-G-A Inborn genetic diseases Uncertain significance (Oct 29, 2021)2378968
19-49010582-G-A Inborn genetic diseases Uncertain significance (Mar 14, 2023)2457449
19-49011063-C-T Benign (Jul 16, 2018)709500
19-49011284-C-G Inborn genetic diseases Uncertain significance (Aug 30, 2022)2387941
19-49014569-A-T Inborn genetic diseases Uncertain significance (Feb 23, 2023)2456729
19-49014596-C-T Inborn genetic diseases Uncertain significance (Feb 22, 2023)2457542
19-49015097-C-T Inborn genetic diseases Uncertain significance (Mar 21, 2022)2398028
19-49015102-C-T Benign (Jun 28, 2018)714008
19-49015139-C-T Inborn genetic diseases Uncertain significance (Oct 26, 2022)2366084
19-49015801-T-C Benign (Aug 09, 2018)1277510
19-49015822-G-A Inborn genetic diseases Uncertain significance (Jul 20, 2021)2238606

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RUVBL2protein_codingprotein_codingENST00000595090 1522548
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.000.0000800124734021247360.00000802
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense3.111783390.5240.00002442989
Missense in Polyphen51156.460.325961287
Synonymous0.04411391400.9950.0000105928
Loss of Function4.79026.80.000.00000137288

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00001020.00000883
Middle Eastern0.000.00
South Asian0.00003280.0000327
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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