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 ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

• Inborn genetic diseases (3 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.

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			3			3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	0	0

Variants in RUVBL1

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

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
3-128064855-A-T		not specified	Benign (Jan 24, 2024)
3-128064858-TCTC-T			Likely benign (Nov 27, 2023)
3-128064861-C-T			Likely benign (Sep 27, 2022)
3-128064865-C-T			Likely benign (Dec 21, 2023)
3-128064879-A-G			Uncertain significance (Aug 17, 2023)
3-128064893-T-G			Likely benign (Oct 13, 2023)
3-128064897-A-G			Uncertain significance (Dec 27, 2023)
3-128064902-C-T			Likely benign (Jul 11, 2022)
3-128064906-C-G			Uncertain significance (Apr 01, 2022)
3-128064911-C-T			Likely benign (Nov 21, 2022)
3-128064913-A-G			Uncertain significance (Sep 24, 2023)
3-128064914-T-A		Inborn genetic diseases	Uncertain significance (Sep 16, 2021)
3-128064917-G-C			Likely benign (Nov 27, 2023)
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 (May 25, 2023)
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 (Feb 08, 2023)
3-128064996-A-C		Inborn genetic diseases	Uncertain significance (Oct 03, 2023)
3-128065005-A-G			Uncertain significance (Feb 23, 2022)
3-128065015-T-C			Uncertain significance (Sep 02, 2022)
3-128065021-T-C			Uncertain significance (Dec 19, 2023)
3-128065024-T-C			Uncertain significance (Jun 24, 2023)

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