RUVBL1

RuvB like AAA ATPase 1, the group of R2SP complex|Tip60/Nua4 histone acetyltransferase complex subunits|INO80 complex |DNA helicases|AAA ATPases|R2TP complex|SRCAP complex

Basic information

Region (hg38): 3:128064777-128153914

Links

ENSG00000175792 ∙ NCBI:8607 ∙ OMIM:603449 ∙ HGNC:10474 ∙ Uniprot:Q9Y265 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RUVBL1 gene.

• not provided (83 variants)
• Inborn genetic diseases (5 variants)
• Autosomal dominant polycystic liver disease (2 variants)
• Hyperuricemic nephropathy, familial juvenile type 4 (1 variants)
• not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RUVBL1 gene is commonly pathogenic or not.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			2	1		3
nonsense				1		1
start loss						0
frameshift						0
inframe indel						0
splice variant						0
non coding		2	29	40	13	84
Total	0	2	31	42	13

Variants in RUVBL1

This is a list of pathogenic ClinVar variants found in the RUVBL1 region.

Position	Type	Phenotype	Significance	ClinVar
3-128064855-A-T			Benign (Jan 25, 2019)
3-128064858-TCTC-T			Likely benign (Oct 30, 2022)
3-128064861-C-T			Likely benign (Sep 27, 2022)
3-128064893-T-G			Likely benign (Aug 09, 2021)
3-128064897-A-G			Uncertain significance (Aug 07, 2022)
3-128064902-C-T			Likely benign (Jul 11, 2022)
3-128064906-C-G			Uncertain significance (Apr 01, 2022)
3-128064911-C-T			Likely benign (Aug 22, 2022)
3-128064914-T-A		Inborn genetic diseases	Uncertain significance (Sep 16, 2021)
3-128064917-G-C			Likely benign (Jul 12, 2022)
3-128064918-C-T			Likely benign (Aug 22, 2022)
3-128064926-A-T			Likely benign (Sep 14, 2022)
3-128064953-G-C			Likely benign (Aug 02, 2022)
3-128064959-G-A			Likely benign (Mar 24, 2021)
3-128064966-C-T		Autosomal dominant polycystic liver disease	Likely pathogenic (Sep 01, 2021)
3-128064967-G-A		Autosomal dominant polycystic liver disease	Uncertain significance (Sep 01, 2021)
3-128064980-C-G			Likely benign (Dec 07, 2018)
3-128065005-A-G			Uncertain significance (Feb 23, 2022)
3-128065015-T-C			Uncertain significance (Sep 02, 2022)
3-128065034-C-T			Likely benign (May 19, 2022)
3-128065057-C-T			Likely benign (Aug 23, 2022)
3-128065275-T-C			Benign (Jan 25, 2019)
3-128065298-G-A			Benign (Jan 06, 2020)
3-128066708-G-A			Benign (Mar 28, 2020)
3-128066758-C-T			Benign (Sep 02, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RUVBL1	protein_coding	protein_coding	ENST00000322623	11	89137

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000982	125726	0	2	125728	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.39	107	261	0.410	0.0000137	2987
Missense in Polyphen		12	83.134	0.14435		937
Synonymous	-0.721	111	102	1.09	0.00000577	884
Loss of Function	4.40	1	24.5	0.0409	0.00000144	281

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)	0.0000177	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Possesses single-stranded DNA-stimulated ATPase and ATP- dependent DNA helicase (3' to 5') 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: May be able to bind plasminogen at cell surface and enhance plasminogen activation.
• Pathway: Wnt signaling pathway - Homo sapiens (human);Gastric Cancer Network 1;DNA Repair;Signaling by WNT;Signal Transduction;Post-translational protein modification;Metabolism of proteins;Chromatin modifying enzymes;Nucleosome assembly;HATs acetylate histones;Telomere Extension By Telomerase;Extension of Telomeres;UCH proteinases;Telomere Maintenance;Chromosome Maintenance;Ub-specific processing proteases;Deposition of new CENPA-containing nucleosomes at the centromere;Deubiquitination;Chromatin organization;C-MYC pathway;Cell Cycle;Integrin-linked kinase signaling;DNA Damage Recognition in GG-NER;Global Genome Nucleotide Excision Repair (GG-NER);Validated targets of C-MYC transcriptional activation;Formation of the beta-catenin:TCF transactivating complex;TCF dependent signaling in response to WNT;Nucleotide Excision Repair (Consensus)

Recessive Scores

• pRec: 0.388

Intolerance Scores

• loftool: 0.233
• rvis_EVS: -0.56
• rvis_percentile_EVS: 19.31

Haploinsufficiency Scores

• pHI: 0.863
• hipred: Y
• hipred_score: 0.802
• ghis: 0.669

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.998

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Low	Low
Primary Immunodeficiency	Medium	Low	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Ruvbl1
• Phenotype: embryo phenotype; hematopoietic 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); immune system phenotype; cellular phenotype; growth/size/body region phenotype

Zebrafish Information Network

• Gene name: ruvbl1
• Affected structure: pronephric tubule
• Phenotype tag: abnormal
• Phenotype quality: immobile

Gene ontology

• Biological process: box C/D snoRNP assembly;DNA repair;DNA recombination;chromatin remodeling;regulation of transcription by RNA polymerase II;cell cycle;spermatogenesis;histone acetylation;protein deubiquitination;DNA duplex unwinding;CENP-A containing nucleosome assembly;regulation of growth;histone H4 acetylation;histone H2A acetylation;cell division;positive regulation of canonical Wnt signaling pathway;positive regulation of nucleic acid-templated transcription;beta-catenin-TCF complex assembly;positive regulation of telomerase RNA localization to Cajal body
• Cellular component: Swr1 complex;nucleus;nucleoplasm;microtubule organizing center;cytosol;membrane;nuclear matrix;Ino80 complex;NuA4 histone acetyltransferase complex;extracellular exosome;MLL1 complex;R2TP complex;ribonucleoprotein complex
• Molecular function: TFIID-class transcription factor complex binding;DNA helicase activity;transcription coactivator activity;ATP-dependent DNA helicase activity;protein binding;ATP binding;ATPase activity;TBP-class protein binding;ATP-dependent 5'-3' DNA helicase activity;ADP binding;cadherin binding;ATPase binding