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Center for Computational Systems Medicine level1
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:BRWD1-CHMP1A

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: BRWD1-CHMP1A
FusionPDB ID: 10340
FusionGDB2.0 ID: 10340
HgeneTgene
Gene symbol

BRWD1

CHMP1A

Gene ID

54014

5119

Gene namebromodomain and WD repeat domain containing 1charged multivesicular body protein 1A
SynonymsC21orf107|DCAF19|N143|WDR9|WRD9CHMP1|PCH8|PCOLN3|PRSM1|VPS46-1|VPS46A
Cytomap

21q22.2

16q24.3

Type of geneprotein-codingprotein-coding
Descriptionbromodomain and WD repeat-containing protein 1WD repeat protein WDR9-form2WD repeat-containing protein 9transcriptional unit N143charged multivesicular body protein 1acharged multivesicular body protein 1/chromatin modifying protein 1chromatin modifying protein 1Aprocollagen (type III) N-endopeptidaseprotease, metallo, 1, 33kDvacuolar protein sorting-associated protein 46-1
Modification date2020031320200313
UniProtAcc

Q9NSI6

Q9HD42

Ensembl transtripts involved in fusion geneENST idsENST00000333229, ENST00000342449, 
ENST00000380800, ENST00000341322, 
ENST00000470108, 		ENST00000547614, 
ENST00000397901, ENST00000535997, 
ENST00000550102, ENST00000253475, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score28 X 28 X 10=784045 X 11 X 21=10395
# samples 3248
** MAII scorelog2(32/7840*10)=-4.61470984411521
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(48/10395*10)=-4.43671154213721
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: BRWD1 [Title/Abstract] AND CHMP1A [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)BRWD1(40670358)-CHMP1A(89713739), # samples:1
Anticipated loss of major functional domain due to fusion event.BRWD1-CHMP1A seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
BRWD1-CHMP1A seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
BRWD1-CHMP1A seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
BRWD1-CHMP1A seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
BRWD1-CHMP1A seems lost the major protein functional domain in Hgene partner, which is a epigenetic factor due to the frame-shifted ORF.
BRWD1-CHMP1A seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
BRWD1-CHMP1A seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
TgeneCHMP1A

GO:0007076

mitotic chromosome condensation

11559747

TgeneCHMP1A

GO:0016192

vesicle-mediated transport

11559748

TgeneCHMP1A

GO:0016458

gene silencing

11559747

TgeneCHMP1A

GO:0045892

negative regulation of transcription, DNA-templated

11559747


check buttonFusion gene breakpoints across BRWD1 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check buttonFusion gene breakpoints across CHMP1A (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


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Fusion Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
check button Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0)
* All genome coordinats were lifted-over on hg19.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChimerDB4Non-CancerTCGA-IN-8462-11ABRWD1chr21

40670358

-CHMP1Achr16

89713739

-


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Fusion ORF Analysis


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)
ENST00000333229BRWD1chr2140670358-ENST00000253475CHMP1Achr1689713739-26446772351167310
ENST00000342449BRWD1chr2140670358-ENST00000253475CHMP1Achr1689713739-239542879918279
ENST00000380800BRWD1chr2140670358-ENST00000253475CHMP1Achr1689713739-24154486938310

check buttonDeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score
ENST00000333229ENST00000253475BRWD1chr2140670358-CHMP1Achr1689713739-0.31443390.68556607
ENST00000342449ENST00000253475BRWD1chr2140670358-CHMP1Achr1689713739-0.329835270.6701647
ENST00000380800ENST00000253475BRWD1chr2140670358-CHMP1Achr1689713739-0.328833220.6711668

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Fusion Amino Acid Sequences


check button For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>10340_10340_1_BRWD1-CHMP1A_BRWD1_chr21_40670358_ENST00000333229_CHMP1A_chr16_89713739_ENST00000253475_length(amino acids)=310AA_BP=147
MRRGDASPVRPRRGLHAPLARSLPPPAPRPAMAEPSSARRPVPLIESELYFLIARYLSAGPCRRAAQVLVQELEQYQLLPKRLDWEGNEH
NRSYEELVLSNKHVAPDHLLQICQRIGPMLDKEIPPSISRVTSLLGAGRQSLLRTAKGDQEYGPGDQSPGQGPEHHGPAEGLLSDGQVRA
AGAEPGRPYIGDGGLHELGHHPDHAAGAGGQPHHADRRGEWPGGAGPAQPAARGRLCRGRELCAQPGGPAVTEVGRLEELAVPRRCAPPL

--------------------------------------------------------------

>10340_10340_2_BRWD1-CHMP1A_BRWD1_chr21_40670358_ENST00000342449_CHMP1A_chr16_89713739_ENST00000253475_length(amino acids)=279AA_BP=116
MAEPSSARRPVPLIESELYFLIARYLSAGPCRRAAQVLVQELEQYQLLPKRLDWEGNEHNRSYEELVLSNKHVAPDHLLQICQRIGPMLD
KEIPPSISRVTSLLGAGRQSLLRTAKGDQEYGPGDQSPGQGPEHHGPAEGLLSDGQVRAAGAEPGRPYIGDGGLHELGHHPDHAAGAGGQ
PHHADRRGEWPGGAGPAQPAARGRLCRGRELCAQPGGPAVTEVGRLEELAVPRRCAPPLPRDVLEGSCPLPTASCLCADPAGLRPAATLR

--------------------------------------------------------------

>10340_10340_3_BRWD1-CHMP1A_BRWD1_chr21_40670358_ENST00000380800_CHMP1A_chr16_89713739_ENST00000253475_length(amino acids)=310AA_BP=147
MRRGDASPVRPRRGLHAPLARSLPPPAPRPAMAEPSSARRPVPLIESELYFLIARYLSAGPCRRAAQVLVQELEQYQLLPKRLDWEGNEH
NRSYEELVLSNKHVAPDHLLQICQRIGPMLDKEIPPSISRVTSLLGAGRQSLLRTAKGDQEYGPGDQSPGQGPEHHGPAEGLLSDGQVRA
AGAEPGRPYIGDGGLHELGHHPDHAAGAGGQPHHADRRGEWPGGAGPAQPAARGRLCRGRELCAQPGGPAVTEVGRLEELAVPRRCAPPL

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Fusion Protein Functional Features


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr21:40670358/chr16:89713739)
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
- How to search
1. Put your fusion gene symbol.
2. Press the tab key until there will be shown the breakpoint information filled.
4. Go down and press 'Search' tab twice.
4. Go down to have the hyperlink of the search result.
5. Click the hyperlink.
6. See the FGviewer result for your fusion gene.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
BRWD1

Q9NSI6

CHMP1A

Q9HD42

FUNCTION: May be a transcriptional activator. May be involved in chromatin remodeling (By similarity). Plays a role in the regulation of cell morphology and cytoskeletal organization. Required in the control of cell shape. {ECO:0000250, ECO:0000269|PubMed:21834987}.FUNCTION: Probable peripherally associated component of the endosomal sorting required for transport complex III (ESCRT-III) which is involved in multivesicular bodies (MVBs) formation and sorting of endosomal cargo proteins into MVBs. MVBs contain intraluminal vesicles (ILVs) that are generated by invagination and scission from the limiting membrane of the endosome and mostly are delivered to lysosomes enabling degradation of membrane proteins, such as stimulated growth factor receptors, lysosomal enzymes and lipids. The MVB pathway appears to require the sequential function of ESCRT-O, -I,-II and -III complexes. ESCRT-III proteins mostly dissociate from the invaginating membrane before the ILV is released. The ESCRT machinery also functions in topologically equivalent membrane fission events, such as the terminal stages of cytokinesis and the budding of enveloped viruses (HIV-1 and other lentiviruses). ESCRT-III proteins are believed to mediate the necessary vesicle extrusion and/or membrane fission activities, possibly in conjunction with the AAA ATPase VPS4. Involved in cytokinesis. Involved in recruiting VPS4A and/or VPS4B to the midbody of dividing cells. May also be involved in chromosome condensation. Targets the Polycomb group (PcG) protein BMI1/PCGF4 to regions of condensed chromatin. May play a role in stable cell cycle progression and in PcG gene silencing. {ECO:0000269|PubMed:11559747, ECO:0000269|PubMed:11559748, ECO:0000269|PubMed:19129479, ECO:0000269|PubMed:23045692}.

check buttonRetention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at

download page

* Minus value of BPloci means that the break pointn is located before the CDS.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
TgeneCHMP1Achr21:40670358chr16:89713739ENST0000039790137102_12484.0197.0Coiled coilOntology_term=ECO:0000255
TgeneCHMP1Achr21:40670358chr16:89713739ENST0000039790137185_19584.0197.0MotifNote=MIT-interacting motif

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneBRWD1chr21:40670358chr16:89713739ENST00000333229-5421539_1548116.333333333333332321.0Compositional biasNote=Poly-Ser
HgeneBRWD1chr21:40670358chr16:89713739ENST00000333229-5421687_1692116.333333333333332321.0Compositional biasNote=Poly-Glu
HgeneBRWD1chr21:40670358chr16:89713739ENST00000333229-542661_668116.333333333333332321.0Compositional biasNote=Poly-Gln
HgeneBRWD1chr21:40670358chr16:89713739ENST00000333229-542821_824116.333333333333332321.0Compositional biasNote=Poly-Ser
HgeneBRWD1chr21:40670358chr16:89713739ENST00000341322-151539_15480121.0Compositional biasNote=Poly-Ser
HgeneBRWD1chr21:40670358chr16:89713739ENST00000341322-151687_16920121.0Compositional biasNote=Poly-Glu
HgeneBRWD1chr21:40670358chr16:89713739ENST00000341322-15661_6680121.0Compositional biasNote=Poly-Gln
HgeneBRWD1chr21:40670358chr16:89713739ENST00000341322-15821_8240121.0Compositional biasNote=Poly-Ser
HgeneBRWD1chr21:40670358chr16:89713739ENST00000342449-5411539_1548116.333333333333332270.0Compositional biasNote=Poly-Ser
HgeneBRWD1chr21:40670358chr16:89713739ENST00000342449-5411687_1692116.333333333333332270.0Compositional biasNote=Poly-Glu
HgeneBRWD1chr21:40670358chr16:89713739ENST00000342449-541661_668116.333333333333332270.0Compositional biasNote=Poly-Gln
HgeneBRWD1chr21:40670358chr16:89713739ENST00000342449-541821_824116.333333333333332270.0Compositional biasNote=Poly-Ser
HgeneBRWD1chr21:40670358chr16:89713739ENST00000380800-5421539_1548116.333333333333332200.0Compositional biasNote=Poly-Ser
HgeneBRWD1chr21:40670358chr16:89713739ENST00000380800-5421687_1692116.333333333333332200.0Compositional biasNote=Poly-Glu
HgeneBRWD1chr21:40670358chr16:89713739ENST00000380800-542661_668116.333333333333332200.0Compositional biasNote=Poly-Gln
HgeneBRWD1chr21:40670358chr16:89713739ENST00000380800-542821_824116.333333333333332200.0Compositional biasNote=Poly-Ser
HgeneBRWD1chr21:40670358chr16:89713739ENST00000333229-5421177_1247116.333333333333332321.0DomainBromo 1
HgeneBRWD1chr21:40670358chr16:89713739ENST00000333229-5421330_1400116.333333333333332321.0DomainBromo 2
HgeneBRWD1chr21:40670358chr16:89713739ENST00000341322-151177_12470121.0DomainBromo 1
HgeneBRWD1chr21:40670358chr16:89713739ENST00000341322-151330_14000121.0DomainBromo 2
HgeneBRWD1chr21:40670358chr16:89713739ENST00000342449-5411177_1247116.333333333333332270.0DomainBromo 1
HgeneBRWD1chr21:40670358chr16:89713739ENST00000342449-5411330_1400116.333333333333332270.0DomainBromo 2
HgeneBRWD1chr21:40670358chr16:89713739ENST00000380800-5421177_1247116.333333333333332200.0DomainBromo 1
HgeneBRWD1chr21:40670358chr16:89713739ENST00000380800-5421330_1400116.333333333333332200.0DomainBromo 2
HgeneBRWD1chr21:40670358chr16:89713739ENST00000333229-542184_223116.333333333333332321.0RepeatNote=WD 1
HgeneBRWD1chr21:40670358chr16:89713739ENST00000333229-542226_265116.333333333333332321.0RepeatNote=WD 2
HgeneBRWD1chr21:40670358chr16:89713739ENST00000333229-542268_311116.333333333333332321.0RepeatNote=WD 3
HgeneBRWD1chr21:40670358chr16:89713739ENST00000333229-542322_365116.333333333333332321.0RepeatNote=WD 4
HgeneBRWD1chr21:40670358chr16:89713739ENST00000333229-542366_405116.333333333333332321.0RepeatNote=WD 5
HgeneBRWD1chr21:40670358chr16:89713739ENST00000333229-542424_463116.333333333333332321.0RepeatNote=WD 6
HgeneBRWD1chr21:40670358chr16:89713739ENST00000333229-542466_506116.333333333333332321.0RepeatNote=WD 7
HgeneBRWD1chr21:40670358chr16:89713739ENST00000333229-542514_553116.333333333333332321.0RepeatNote=WD 8
HgeneBRWD1chr21:40670358chr16:89713739ENST00000341322-15184_2230121.0RepeatNote=WD 1
HgeneBRWD1chr21:40670358chr16:89713739ENST00000341322-15226_2650121.0RepeatNote=WD 2
HgeneBRWD1chr21:40670358chr16:89713739ENST00000341322-15268_3110121.0RepeatNote=WD 3
HgeneBRWD1chr21:40670358chr16:89713739ENST00000341322-15322_3650121.0RepeatNote=WD 4
HgeneBRWD1chr21:40670358chr16:89713739ENST00000341322-15366_4050121.0RepeatNote=WD 5
HgeneBRWD1chr21:40670358chr16:89713739ENST00000341322-15424_4630121.0RepeatNote=WD 6
HgeneBRWD1chr21:40670358chr16:89713739ENST00000341322-15466_5060121.0RepeatNote=WD 7
HgeneBRWD1chr21:40670358chr16:89713739ENST00000341322-15514_5530121.0RepeatNote=WD 8
HgeneBRWD1chr21:40670358chr16:89713739ENST00000342449-541184_223116.333333333333332270.0RepeatNote=WD 1
HgeneBRWD1chr21:40670358chr16:89713739ENST00000342449-541226_265116.333333333333332270.0RepeatNote=WD 2
HgeneBRWD1chr21:40670358chr16:89713739ENST00000342449-541268_311116.333333333333332270.0RepeatNote=WD 3
HgeneBRWD1chr21:40670358chr16:89713739ENST00000342449-541322_365116.333333333333332270.0RepeatNote=WD 4
HgeneBRWD1chr21:40670358chr16:89713739ENST00000342449-541366_405116.333333333333332270.0RepeatNote=WD 5
HgeneBRWD1chr21:40670358chr16:89713739ENST00000342449-541424_463116.333333333333332270.0RepeatNote=WD 6
HgeneBRWD1chr21:40670358chr16:89713739ENST00000342449-541466_506116.333333333333332270.0RepeatNote=WD 7
HgeneBRWD1chr21:40670358chr16:89713739ENST00000342449-541514_553116.333333333333332270.0RepeatNote=WD 8
HgeneBRWD1chr21:40670358chr16:89713739ENST00000380800-542184_223116.333333333333332200.0RepeatNote=WD 1
HgeneBRWD1chr21:40670358chr16:89713739ENST00000380800-542226_265116.333333333333332200.0RepeatNote=WD 2
HgeneBRWD1chr21:40670358chr16:89713739ENST00000380800-542268_311116.333333333333332200.0RepeatNote=WD 3
HgeneBRWD1chr21:40670358chr16:89713739ENST00000380800-542322_365116.333333333333332200.0RepeatNote=WD 4
HgeneBRWD1chr21:40670358chr16:89713739ENST00000380800-542366_405116.333333333333332200.0RepeatNote=WD 5
HgeneBRWD1chr21:40670358chr16:89713739ENST00000380800-542424_463116.333333333333332200.0RepeatNote=WD 6
HgeneBRWD1chr21:40670358chr16:89713739ENST00000380800-542466_506116.333333333333332200.0RepeatNote=WD 7
HgeneBRWD1chr21:40670358chr16:89713739ENST00000380800-542514_553116.333333333333332200.0RepeatNote=WD 8
TgeneCHMP1Achr21:40670358chr16:89713739ENST00000397901375_4784.0197.0Coiled coilOntology_term=ECO:0000255


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Fusion Protein-Protein Interaction


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page.


check button Protein-protein interactors with each fusion partner protein in wild-type from validated records (BIOGRID-3.4.160)
GenePPI interactors


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
BRWD1
CHMP1A


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs to BRWD1-CHMP1A


check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

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Related Diseases to BRWD1-CHMP1A


check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource