RGD Reference Report - The spectrum of SWI/SNF mutations, ubiquitous in human cancers. - Rat Genome Database

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The spectrum of SWI/SNF mutations, ubiquitous in human cancers.

Authors: Shain, AH  Pollack, JR 
Citation: Shain AH and Pollack JR, PLoS One. 2013;8(1):e55119. doi: 10.1371/journal.pone.0055119. Epub 2013 Jan 23.
RGD ID: 8694154
Pubmed: PMID:23355908   (View Abstract at PubMed)
PMCID: PMC3552954   (View Article at PubMed Central)
DOI: DOI:10.1371/journal.pone.0055119   (Journal Full-text)

SWI/SNF is a multi-subunit chromatin remodeling complex that uses the energy of ATP hydrolysis to reposition nucleosomes, thereby modulating gene expression. Accumulating evidence suggests that SWI/SNF functions as a tumor suppressor in some cancers. However, the spectrum of SWI/SNF mutations across human cancers has not been systematically investigated. Here, we mined whole-exome sequencing data from 24 published studies representing 669 cases from 18 neoplastic diagnoses. SWI/SNF mutations were widespread across diverse human cancers, with an excess of deleterious mutations, and an overall frequency approaching TP53 mutation. Mutations occurred most commonly in the SMARCA4 enzymatic subunit, and in subunits thought to confer functional specificity (ARID1A, ARID1B, PBRM1, and ARID2). SWI/SNF mutations were not mutually-exclusive of other mutated cancer genes, including TP53 and EZH2 (both previously linked to SWI/SNF). Our findings implicate SWI/SNF as an important but under-recognized tumor suppressor in diverse human cancers, and provide a key resource to guide future investigations.

RGD Manual Disease Annotations    Click to see Annotation Detail View

Molecular Pathway Annotations    Click to see Annotation Detail View

RGD Manual Annotations

TermQualifierEvidenceWithReferenceNotesSourceOriginal Reference(s)
altered SWI/SNF family mediated chromatin remodeling pathway  TAS 8694154; 8694154; 8694154; 8694154; 8694154 RGD 
altered SWI/SNF family mediated chromatin remodeling pathway  ISOACTL6A (Homo sapiens)8694154; 8694154 RGD 
altered SWI/SNF family mediated chromatin remodeling pathway  ISOARID1A (Homo sapiens)8694154; 8694154 RGD 
altered SWI/SNF family mediated chromatin remodeling pathway  ISOARID1B (Homo sapiens)8694154; 8694154 RGD 
altered SWI/SNF family mediated chromatin remodeling pathway  ISOPBRM1 (Homo sapiens)8694154; 8694154 RGD 
altered SWI/SNF family mediated chromatin remodeling pathway  ISOSMARCA4 (Homo sapiens)8694154; 8694154 RGD 
pancreatic cancer pathway   TAS 8694154; 8694154; 8694154; 8694154; 8694154 RGD 
pancreatic cancer pathway   ISOACTL6A (Homo sapiens)8694154; 8694154 RGD 
pancreatic cancer pathway   ISOARID1A (Homo sapiens)8694154; 8694154 RGD 
pancreatic cancer pathway   ISOARID1B (Homo sapiens)8694154; 8694154 RGD 
pancreatic cancer pathway   ISOPBRM1 (Homo sapiens)8694154; 8694154 RGD 
pancreatic cancer pathway   ISOSMARCA4 (Homo sapiens)8694154; 8694154 RGD 
SWI/SNF family mediated chromatin remodeling pathway  TAS 8694154; 8694154; 8694154; 8694154; 8694154; 8694154; 8694154; 8694154; 8694154; 8694154; 8694154; 8694154; 8694154; 8694154; 8694154; 8694154; 8694154; 8694154; 8694154; 8694154 RGD 
SWI/SNF family mediated chromatin remodeling pathway  ISOACTL6A (Homo sapiens)8694154; 8694154 RGD 
SWI/SNF family mediated chromatin remodeling pathway  ISOACTL6B (Homo sapiens)8694154; 8694154 RGD 
SWI/SNF family mediated chromatin remodeling pathway  ISOARID1A (Homo sapiens)8694154; 8694154; 8694154; 8694154 RGD 
SWI/SNF family mediated chromatin remodeling pathway  ISOARID1B (Homo sapiens)8694154; 8694154 RGD 
SWI/SNF family mediated chromatin remodeling pathway  ISOBRD7 (Homo sapiens)8694154; 8694154 RGD 
SWI/SNF family mediated chromatin remodeling pathway  ISODPF1 (Homo sapiens)8694154; 8694154 RGD 
SWI/SNF family mediated chromatin remodeling pathway  ISODPF2 (Homo sapiens)8694154; 8694154 RGD 
SWI/SNF family mediated chromatin remodeling pathway  ISODPF3 (Homo sapiens)8694154; 8694154 RGD 
SWI/SNF family mediated chromatin remodeling pathway  ISOPBRM1 (Homo sapiens)8694154; 8694154 RGD 
SWI/SNF family mediated chromatin remodeling pathway  ISOPHF10 (Homo sapiens)8694154; 8694154 RGD 
SWI/SNF family mediated chromatin remodeling pathway  ISOSMARCA2 (Homo sapiens)8694154; 8694154 RGD 
SWI/SNF family mediated chromatin remodeling pathway  ISOSMARCA4 (Homo sapiens)8694154; 8694154 RGD 
SWI/SNF family mediated chromatin remodeling pathway  ISOSMARCB1 (Homo sapiens)8694154; 8694154 RGD 
SWI/SNF family mediated chromatin remodeling pathway  ISOSMARCC1 (Homo sapiens)8694154; 8694154 RGD 
SWI/SNF family mediated chromatin remodeling pathway  ISOSMARCC2 (Homo sapiens)8694154; 8694154 RGD 
SWI/SNF family mediated chromatin remodeling pathway  ISOSMARCD1 (Homo sapiens)8694154; 8694154 RGD 
SWI/SNF family mediated chromatin remodeling pathway  ISOSMARCD2 (Homo sapiens)8694154; 8694154 RGD 
SWI/SNF family mediated chromatin remodeling pathway  ISOSMARCD3 (Homo sapiens)8694154; 8694154 RGD 
SWI/SNF family mediated chromatin remodeling pathway  ISOSMARCE1 (Homo sapiens)8694154; 8694154 RGD 
Objects Annotated

Genes (Rattus norvegicus)
Actl6a  (actin-like 6A)
Actl6b  (actin-like 6B)
Arid1a  (AT-rich interaction domain 1A)
Arid1b  (AT-rich interaction domain 1B)
Arid2  (AT-rich interaction domain 2)
Brd7  (bromodomain containing 7)
Dpf1  (double PHD fingers 1)
Dpf2  (double PHD fingers 2)
Dpf3  (double PHD fingers 3)
Pbrm1  (polybromo 1)
Phf10  (PHD finger protein 10)
Smarca2  (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2)
Smarca4  (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4)
Smarcb1  (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1)
Smarcc1  (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 1)
Smarcc2  (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2)
Smarcd1  (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1)
Smarcd2  (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 2)
Smarcd3  (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3)
Smarce1  (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1)

Genes (Mus musculus)
Actl6a  (actin-like 6A)
Actl6b  (actin-like 6B)
Arid1a  (AT-rich interaction domain 1A)
Arid1b  (AT-rich interaction domain 1B)
Arid2  (AT-rich interaction domain 2)
Brd7  (bromodomain containing 7)
Dpf1  (double PHD fingers 1)
Dpf2  (double PHD fingers 2)
Dpf3  (double PHD fingers 3)
Pbrm1  (polybromo 1)
Phf10  (PHD finger protein 10)
Smarca2  (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2)
Smarca4  (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4)
Smarcb1  (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1)
Smarcc1  (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 1)
Smarcc2  (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2)
Smarcd1  (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1)
Smarcd2  (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 2)
Smarcd3  (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3)
Smarce1  (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1)

Genes (Homo sapiens)
ACTL6A  (actin like 6A)
ACTL6B  (actin like 6B)
ARID1A  (AT-rich interaction domain 1A)
ARID1B  (AT-rich interaction domain 1B)
ARID2  (AT-rich interaction domain 2)
BRD7  (bromodomain containing 7)
DPF1  (double PHD fingers 1)
DPF2  (double PHD fingers 2)
DPF3  (double PHD fingers 3)
PBRM1  (polybromo 1)
PHF10  (PHD finger protein 10)
SMARCA2  (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2)
SMARCA4  (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4)
SMARCB1  (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1)
SMARCC1  (SWI/SNF related, matrix associated, actin dependent regulator of chromatin subfamily c member 1)
SMARCC2  (SWI/SNF related, matrix associated, actin dependent regulator of chromatin subfamily c member 2)
SMARCD1  (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1)
SMARCD2  (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 2)
SMARCD3  (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3)
SMARCE1  (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1)


Additional Information