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Aliases for PBRM1 Gene

Aliases for PBRM1 Gene

  • Polybromo 1 2 3 5
  • BRG1-Associated Factor 180 3 4
  • Polybromo-1D 3 4
  • BAF180 3 4
  • PB1 3 4
  • Protein Polybromo-1 3
  • HPB1 4

External Ids for PBRM1 Gene

Previous GeneCards Identifiers for PBRM1 Gene

  • GC03M052554

Summaries for PBRM1 Gene

Entrez Gene Summary for PBRM1 Gene

  • This locus encodes a subunit of ATP-dependent chromatin-remodeling complexes. The encoded protein has been identified as in integral component of complexes necessary for ligand-dependent transcriptional activation by nuclear hormone receptors. Mutations at this locus have been associated with primary clear cell renal cell carcinoma. [provided by RefSeq, Feb 2012]

CIViC summary for PBRM1 Gene

GeneCards Summary for PBRM1 Gene

PBRM1 (Polybromo 1) is a Protein Coding gene. Diseases associated with PBRM1 include Renal Clear Cell Carcinoma and Renal Cell Carcinoma. Among its related pathways are Chromatin organization and Apoptosis Modulation and Signaling. GO annotations related to this gene include chromatin binding.

UniProtKB/Swiss-Prot for PBRM1 Gene

  • Involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology). Acts as a negative regulator of cell proliferation.

Gene Wiki entry for PBRM1 Gene

Additional gene information for PBRM1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PBRM1 Gene

Genomics for PBRM1 Gene

Regulatory Elements for PBRM1 Gene

Enhancers for PBRM1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH03H053345 1.5 FANTOM5 ENCODE 45.7 -661.4 -661409 2 MLX ZFP64 FEZF1 DMAP1 YY1 ZNF416 ZNF143 SP3 NFYC ZC3H11A PBRM1 NISCH LOC101059924 ENSG00000271976 PHF7 CABYRP1 RFT1 DCP1A ENSG00000212608 PRKCD
GH03H052683 1.4 ENCODE dbSUPER 45 -0.4 -404 5 HDGF PKNOX1 MLX ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF766 PBRM1 GNL3 RFT1 RRP9 ABHD14B ITIH1 ENSG00000280904
GH03H052769 1.1 ENCODE 50 -85.0 -84971 2 HDGF FOXA2 ARID4B SIN3A DMAP1 YY1 SLC30A9 ZNF207 ZNF143 SP3 PBRM1 RFT1 ITIH3 RRP9 ITIH4-AS1 ENSG00000243696 ITIH4 SNORD69 GNL3 MUSTN1
GH03H052274 1.7 Ensembl ENCODE dbSUPER 30.6 +403.1 403063 17 HDGF PKNOX1 FOXA2 MLX ARNT ARID4B SIN3A DMAP1 YY1 SLC30A9 PBRM1 LOC101929054 PPM1M TWF2 ITIH4 GLYCTK RRP9 RFT1 RAD54L2 DCAF1
GH03H052681 1.5 Ensembl ENCODE dbSUPER 31.1 +4.1 4087 2 FOXA2 ATF1 MLX SIN3A ARID4B DMAP1 YY1 ZNF143 RUNX3 MXD4 PBRM1 ITIH4 NT5DC2 GNL3 ITIH1
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around PBRM1 on UCSC Golden Path with GeneCards custom track

Promoters for PBRM1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000152582 117 2401 HDGF PKNOX1 MLX ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF766

Transcription factor binding sites by QIAGEN in the PBRM1 gene promoter:

Genomic Location for PBRM1 Gene

Chromosome:
3
Start:
52,545,352 bp from pter
End:
52,685,917 bp from pter
Size:
140,566 bases
Orientation:
Minus strand

Genomic View for PBRM1 Gene

Genes around PBRM1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PBRM1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PBRM1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PBRM1 Gene

Proteins for PBRM1 Gene

  • Protein details for PBRM1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q86U86-PB1_HUMAN
    Recommended name:
    Protein polybromo-1
    Protein Accession:
    Q86U86
    Secondary Accessions:
    • A1L381
    • A1L382
    • A4FUJ7
    • Q1RMD1
    • Q1RMD2
    • Q96MS2
    • Q9H2T3
    • Q9H2T4
    • Q9H2T5
    • Q9H301
    • Q9H314

    Protein attributes for PBRM1 Gene

    Size:
    1689 amino acids
    Molecular mass:
    192948 Da
    Quaternary structure:
    • Component of the SWI/SNF-B (PBAF) chromatin-remodeling complex, which contains at least SMARCA4/BRG1, SMARCB1/SNF5/INI1/BAF47, ACTL6A/BAF53A or ACTL6B/BAF53B, SMARCE1/BAF57, SMARCD1/BAF60A, SMARCD2/BAF60B, perhaps SMARCD3/BAF60C, SMARCC1/BAF155, SMARCC2/BAF170, PB1/BAF180, ARID2/BAF200, ARID1A/BAF250A or ARID1B/BAF250B and actin. Interacts with PHF10/BAF45A (By similarity). Interacts with acetylated Lys-14 of histone H3 (H3K14ac), and may also interact with other acetylated or methylated Lys residues on histone H3.
    SequenceCaution:
    • Sequence=AAI15010.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence.; Evidence={ECO:0000305}; Sequence=AAI15011.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=AAI15012.1; Type=Erroneous termination; Positions=78; Note=Translated as Arg.; Evidence={ECO:0000305}; Sequence=BAB71210.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for PBRM1 Gene

    Alternative splice isoforms for PBRM1 Gene

neXtProt entry for PBRM1 Gene

Post-translational modifications for PBRM1 Gene

  • Ubiquitination at posLast=754754, Lys1398, posLast=16261626, and posLast=16421642
  • Modification sites at PhosphoSitePlus

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for PBRM1 (polybromo 1)

No data available for DME Specific Peptides for PBRM1 Gene

Domains & Families for PBRM1 Gene

Gene Families for PBRM1 Gene

Human Protein Atlas (HPA):
  • Cancer-related genes
  • Disease related genes
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for PBRM1 Gene

Suggested Antigen Peptide Sequences for PBRM1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with PBRM1: view

No data available for UniProtKB/Swiss-Prot for PBRM1 Gene

Function for PBRM1 Gene

Molecular function for PBRM1 Gene

UniProtKB/Swiss-Prot Function:
Involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology). Acts as a negative regulator of cell proliferation.

Phenotypes From GWAS Catalog for PBRM1 Gene

Gene Ontology (GO) - Molecular Function for PBRM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0003682 chromatin binding NAS,IEA 11078522
GO:0005515 protein binding IPI 11780067
genes like me logo Genes that share ontologies with PBRM1: view
genes like me logo Genes that share phenotypes with PBRM1: view

Animal Models for PBRM1 Gene

MGI Knock Outs for PBRM1:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for PBRM1
  • Applied Biological Materials Clones for PBRM1
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for PBRM1 Gene

Localization for PBRM1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PBRM1 Gene

Nucleus.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PBRM1 gene
Compartment Confidence
nucleus 5
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for PBRM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000228 nuclear chromosome NAS 11078522
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm IDA --
GO:0090544 BAF-type complex IDA 12368262
genes like me logo Genes that share ontologies with PBRM1: view

Pathways & Interactions for PBRM1 Gene

genes like me logo Genes that share pathways with PBRM1: view

Pathways by source for PBRM1 Gene

1 Sino Biological pathway for PBRM1 Gene

SIGNOR curated interactions for PBRM1 Gene

Activates:

Gene Ontology (GO) - Biological Process for PBRM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000278 mitotic cell cycle TAS 11078522
GO:0006338 chromatin remodeling TAS 11078522
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0008285 negative regulation of cell proliferation IMP 21248752
genes like me logo Genes that share ontologies with PBRM1: view

Drugs & Compounds for PBRM1 Gene

(2) Drugs for PBRM1 Gene - From: DrugBank and ApexBio

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Ribavirin Approved Pharma Target, inhibitor 1011
PFI 3 Pharma inhibitor of polybromo 1 and SMARCA4 0

(1) ApexBio Compounds for PBRM1 Gene

Compound Action Cas Number
PFI 3 inhibitor of polybromo 1 and SMARCA4
genes like me logo Genes that share compounds with PBRM1: view

Drug Products

Transcripts for PBRM1 Gene

Unigene Clusters for PBRM1 Gene

Polybromo 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for PBRM1
  • Applied Biological Materials Clones for PBRM1
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

Alternative Splicing Database (ASD) splice patterns (SP) for PBRM1 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15a · 15b ^ 16a · 16b · 16c ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^ 22 ^ 23a ·
SP1: - -
SP2:
SP3:
SP4:
SP5: -
SP6:
SP7: -

ExUns: 23b ^ 24 ^ 25 ^ 26 ^ 27 ^ 28 ^ 29 ^ 30 ^ 31a · 31b ^ 32
SP1: - -
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:

Relevant External Links for PBRM1 Gene

GeneLoc Exon Structure for
PBRM1
ECgene alternative splicing isoforms for
PBRM1

Expression for PBRM1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PBRM1 Gene

Protein differential expression in normal tissues from HIPED for PBRM1 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (24.9) and CD8 Tcells (8.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for PBRM1 Gene



Protein tissue co-expression partners for PBRM1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PBRM1 Gene:

PBRM1

SOURCE GeneReport for Unigene cluster for PBRM1 Gene:

Hs.189920

mRNA Expression by UniProt/SwissProt for PBRM1 Gene:

Q86U86-PB1_HUMAN
Tissue specificity: Widely expressed.

Evidence on tissue expression from TISSUES for PBRM1 Gene

  • Liver(4.3)
  • Nervous system(2.5)
  • Kidney(2.2)
  • Gall bladder(2.1)
genes like me logo Genes that share expression patterns with PBRM1: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for PBRM1 Gene

Orthologs for PBRM1 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for PBRM1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PBRM1 33 34
  • 99.83 (n)
cow
(Bos Taurus)
Mammalia PBRM1 33 34
  • 94.03 (n)
dog
(Canis familiaris)
Mammalia PBRM1 33 34
  • 93.78 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 93 (a)
OneToMany
-- 34
  • 91 (a)
OneToMany
-- 34
  • 90 (a)
OneToMany
-- 34
  • 85 (a)
OneToMany
-- 34
  • 85 (a)
OneToMany
-- 34
  • 84 (a)
OneToMany
-- 34
  • 64 (a)
OneToMany
mouse
(Mus musculus)
Mammalia Pbrm1 33 16 34
  • 92.5 (n)
rat
(Rattus norvegicus)
Mammalia Pbrm1 33
  • 91.66 (n)
oppossum
(Monodelphis domestica)
Mammalia PBRM1 34
  • 87 (a)
OneToOne
chicken
(Gallus gallus)
Aves PBRM1 33 34
  • 81.75 (n)
lizard
(Anolis carolinensis)
Reptilia PBRM1 34
  • 82 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia pbrm1 33
  • 75.92 (n)
Str.6674 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.7528 33
zebrafish
(Danio rerio)
Actinopterygii PBRM1 (1 of 2) 34
  • 73 (a)
OneToMany
pbrm1 33
  • 70.22 (n)
pbrm1l 34
  • 63 (a)
OneToMany
Dr.13233 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP001099 33
  • 50.69 (n)
fruit fly
(Drosophila melanogaster)
Insecta polybromo 33 34
  • 49.47 (n)
worm
(Caenorhabditis elegans)
Secernentea pbrm-1 33 34
  • 47.25 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RSC2 34
  • 12 (a)
OneToMany
RSC1 34 36
  • 10 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 36 (a)
OneToOne
Species where no ortholog for PBRM1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for PBRM1 Gene

ENSEMBL:
Gene Tree for PBRM1 (if available)
TreeFam:
Gene Tree for PBRM1 (if available)

Paralogs for PBRM1 Gene

(2) SIMAP similar genes for PBRM1 Gene using alignment to 9 proteins:

genes like me logo Genes that share paralogs with PBRM1: view

No data available for Paralogs for PBRM1 Gene

Variants for PBRM1 Gene

Sequence variations from dbSNP and Humsavar for PBRM1 Gene

SNP ID Clin Chr 03 pos Sequence Context AA Info Type
rs864321679 Pathogenic 52,563,364(-) AGAAG(-/ATAGTGAG)GTCAT nc-transcript-variant, reference, frameshift-variant
rs142726131 untested 52,550,462(+) ACTCC(A/G)CACTG nc-transcript-variant, reference, missense
rs201397730 untested 52,548,224(+) GACGT(C/T)GCGTC nc-transcript-variant, reference, missense
rs373477703 untested 52,634,806(+) CTTCA(C/G/T)AGCGT nc-transcript-variant, reference, missense
rs547790173 untested 52,642,043(+) TTTTA(C/T)TACTA nc-transcript-variant, reference, missense

Structural Variations from Database of Genomic Variants (DGV) for PBRM1 Gene

Variant ID Type Subtype PubMed ID
dgv21e194 CNV deletion 18987734
esv1488186 CNV deletion 17803354
esv2442255 CNV deletion 19546169
esv2671058 CNV deletion 23128226
esv2725278 CNV deletion 23290073
esv3156 CNV loss 18987735
esv3561886 CNV deletion 23714750
esv3561888 CNV deletion 23714750
esv8459 CNV gain 19470904
esv9375 CNV loss 19470904
nsv1073644 CNV deletion 25765185
nsv1109514 CNV deletion 24896259
nsv1114379 CNV deletion 24896259
nsv1114380 CNV deletion 24896259
nsv508927 CNV insertion 20534489
nsv822091 CNV loss 20364138
nsv822092 CNV loss 20364138
nsv834697 CNV loss 17160897
nsv956274 CNV deletion 24416366

Variation tolerance for PBRM1 Gene

Residual Variation Intolerance Score: 1.35% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.46; 54.87% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PBRM1 Gene

Human Gene Mutation Database (HGMD)
PBRM1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PBRM1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PBRM1 Gene

Disorders for PBRM1 Gene

MalaCards: The human disease database

(7) MalaCards diseases for PBRM1 Gene - From: HGMD, ClinVar, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
renal clear cell carcinoma
  • clear cell carcinoma of kidney
renal cell carcinoma
  • renal cell carcinoma, clear cell, somatic
clear cell renal cell carcinoma
  • clear cell rcc
clear cell papillary renal cell carcinoma
collecting duct carcinoma
  • carcinoma of renal collecting duct
- elite association - COSMIC cancer census association via MalaCards
Search PBRM1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

PB1_HUMAN
  • Renal cell carcinoma (RCC) [MIM:144700]: Renal cell carcinoma is a heterogeneous group of sporadic or hereditary carcinoma derived from cells of the proximal renal tubular epithelium. It is subclassified into clear cell renal carcinoma (non-papillary carcinoma), papillary renal cell carcinoma, chromophobe renal cell carcinoma, collecting duct carcinoma with medullary carcinoma of the kidney, and unclassified renal cell carcinoma. Clear cell renal cell carcinoma is the most common subtype. {ECO:0000269 PubMed:21248752}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for PBRM1

Genetic Association Database (GAD)
PBRM1
Human Genome Epidemiology (HuGE) Navigator
PBRM1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PBRM1
genes like me logo Genes that share disorders with PBRM1: view

No data available for Genatlas for PBRM1 Gene

Publications for PBRM1 Gene

  1. The 3p21 candidate tumor suppressor gene BAF180 is normally expressed in human lung cancer. (PMID: 15735765) Sekine I … Minna JD (Oncogene 2005) 3 4 22 60
  2. The human SWI/SNF-B chromatin-remodeling complex is related to yeast rsc and localizes at kinetochores of mitotic chromosomes. (PMID: 11078522) Xue Y … Wang W (Proceedings of the National Academy of Sciences of the United States of America 2000) 2 3 4 60
  3. Novel loci for adiponectin levels and their influence on type 2 diabetes and metabolic traits: a multi-ethnic meta-analysis of 45,891 individuals. (PMID: 22479202) Dastani Z … Kathiresan S (PLoS genetics 2012) 3 45 60
  4. Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma. (PMID: 21248752) Varela I … Futreal PA (Nature 2011) 3 4 60
  5. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 45 60

Products for PBRM1 Gene

  • Addgene plasmids for PBRM1

Sources for PBRM1 Gene

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