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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:SBNO2-HMHA1 (FusionGDB2 ID:79359)

Fusion Gene Summary for SBNO2-HMHA1

check button Fusion gene summary
Fusion gene informationFusion gene name: SBNO2-HMHA1
Fusion gene ID: 79359
HgeneTgene
Gene symbol

SBNO2

HMHA1

Gene ID

22904

23526

Gene namestrawberry notch homolog 2Rho GTPase activating protein 45
SynonymsKIAA0963|SNO|STNOHA-1|HLA-HA1|HMHA1
Cytomap

19p13.3

19p13.3

Type of geneprotein-codingprotein-coding
Descriptionprotein strawberry notch homolog 2rho GTPase-activating protein 45histocompatibility (minor) HA-1minor histocompatibility antigen HA-1minor histocompatibility protein HA-1
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000361757, ENST00000438103, 
ENST00000587024, 		ENST00000590577, 
ENST00000591169, ENST00000592335, 
ENST00000313093, ENST00000539243, 
ENST00000543365, ENST00000586866, 
ENST00000590214, ENST00000536472, 
Fusion gene scores* DoF score29 X 15 X 16=69605 X 8 X 6=240
# samples 389
** MAII scorelog2(38/6960*10)=-4.19501598240514
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(9/240*10)=-1.41503749927884
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: SBNO2 [Title/Abstract] AND HMHA1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointSBNO2(1116020)-HMHA1(1080463), # samples:2
Anticipated loss of major functional domain due to fusion event.SBNO2-HMHA1 seems lost the major protein functional domain in Tgene partner, which is a essential gene 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
HgeneSBNO2

GO:0071354

cellular response to interleukin-6

25903009


check buttonFusion gene breakpoints across SBNO2 (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 HMHA1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

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
ChimerDB4BRCATCGA-OL-A5D7-01ASBNO2chr19

1108378

-HMHA1chr19

1077856

+
ChimerDB4HNSCTCGA-UF-A7JC-01ASBNO2chr19

1116020

-HMHA1chr19

1080463

+
ChimerDB4HNSCTCGA-UF-A7JCSBNO2chr19

1116020

-HMHA1chr19

1080463

+


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Fusion Gene ORF analysis for SBNO2-HMHA1

check button Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand
5CDS-intronENST00000361757ENST00000590577SBNO2chr19

1116020

-HMHA1chr19

1080463

+
5CDS-intronENST00000361757ENST00000591169SBNO2chr19

1116020

-HMHA1chr19

1080463

+
5CDS-intronENST00000361757ENST00000592335SBNO2chr19

1116020

-HMHA1chr19

1080463

+
5CDS-intronENST00000438103ENST00000590577SBNO2chr19

1116020

-HMHA1chr19

1080463

+
5CDS-intronENST00000438103ENST00000591169SBNO2chr19

1116020

-HMHA1chr19

1080463

+
5CDS-intronENST00000438103ENST00000592335SBNO2chr19

1116020

-HMHA1chr19

1080463

+
5CDS-intronENST00000587024ENST00000590577SBNO2chr19

1116020

-HMHA1chr19

1080463

+
5CDS-intronENST00000587024ENST00000591169SBNO2chr19

1116020

-HMHA1chr19

1080463

+
5CDS-intronENST00000587024ENST00000592335SBNO2chr19

1116020

-HMHA1chr19

1080463

+
Frame-shiftENST00000361757ENST00000313093SBNO2chr19

1116020

-HMHA1chr19

1080463

+
Frame-shiftENST00000361757ENST00000539243SBNO2chr19

1116020

-HMHA1chr19

1080463

+
Frame-shiftENST00000361757ENST00000543365SBNO2chr19

1116020

-HMHA1chr19

1080463

+
Frame-shiftENST00000361757ENST00000586866SBNO2chr19

1116020

-HMHA1chr19

1080463

+
Frame-shiftENST00000361757ENST00000590214SBNO2chr19

1116020

-HMHA1chr19

1080463

+
Frame-shiftENST00000438103ENST00000536472SBNO2chr19

1116020

-HMHA1chr19

1080463

+
Frame-shiftENST00000587024ENST00000313093SBNO2chr19

1116020

-HMHA1chr19

1080463

+
Frame-shiftENST00000587024ENST00000539243SBNO2chr19

1116020

-HMHA1chr19

1080463

+
Frame-shiftENST00000587024ENST00000543365SBNO2chr19

1116020

-HMHA1chr19

1080463

+
Frame-shiftENST00000587024ENST00000586866SBNO2chr19

1116020

-HMHA1chr19

1080463

+
Frame-shiftENST00000587024ENST00000590214SBNO2chr19

1116020

-HMHA1chr19

1080463

+
In-frameENST00000361757ENST00000536472SBNO2chr19

1116020

-HMHA1chr19

1080463

+
In-frameENST00000438103ENST00000313093SBNO2chr19

1116020

-HMHA1chr19

1080463

+
In-frameENST00000438103ENST00000539243SBNO2chr19

1116020

-HMHA1chr19

1080463

+
In-frameENST00000438103ENST00000543365SBNO2chr19

1116020

-HMHA1chr19

1080463

+
In-frameENST00000438103ENST00000586866SBNO2chr19

1116020

-HMHA1chr19

1080463

+
In-frameENST00000438103ENST00000590214SBNO2chr19

1116020

-HMHA1chr19

1080463

+
In-frameENST00000587024ENST00000536472SBNO2chr19

1116020

-HMHA1chr19

1080463

+
intron-3CDSENST00000361757ENST00000313093SBNO2chr19

1108378

-HMHA1chr19

1077856

+
intron-3CDSENST00000361757ENST00000536472SBNO2chr19

1108378

-HMHA1chr19

1077856

+
intron-3CDSENST00000361757ENST00000539243SBNO2chr19

1108378

-HMHA1chr19

1077856

+
intron-3CDSENST00000361757ENST00000543365SBNO2chr19

1108378

-HMHA1chr19

1077856

+
intron-3CDSENST00000361757ENST00000586866SBNO2chr19

1108378

-HMHA1chr19

1077856

+
intron-3CDSENST00000361757ENST00000590214SBNO2chr19

1108378

-HMHA1chr19

1077856

+
intron-3CDSENST00000438103ENST00000313093SBNO2chr19

1108378

-HMHA1chr19

1077856

+
intron-3CDSENST00000438103ENST00000536472SBNO2chr19

1108378

-HMHA1chr19

1077856

+
intron-3CDSENST00000438103ENST00000539243SBNO2chr19

1108378

-HMHA1chr19

1077856

+
intron-3CDSENST00000438103ENST00000543365SBNO2chr19

1108378

-HMHA1chr19

1077856

+
intron-3CDSENST00000438103ENST00000586866SBNO2chr19

1108378

-HMHA1chr19

1077856

+
intron-3CDSENST00000438103ENST00000590214SBNO2chr19

1108378

-HMHA1chr19

1077856

+
intron-3CDSENST00000587024ENST00000313093SBNO2chr19

1108378

-HMHA1chr19

1077856

+
intron-3CDSENST00000587024ENST00000536472SBNO2chr19

1108378

-HMHA1chr19

1077856

+
intron-3CDSENST00000587024ENST00000539243SBNO2chr19

1108378

-HMHA1chr19

1077856

+
intron-3CDSENST00000587024ENST00000543365SBNO2chr19

1108378

-HMHA1chr19

1077856

+
intron-3CDSENST00000587024ENST00000586866SBNO2chr19

1108378

-HMHA1chr19

1077856

+
intron-3CDSENST00000587024ENST00000590214SBNO2chr19

1108378

-HMHA1chr19

1077856

+
intron-intronENST00000361757ENST00000590577SBNO2chr19

1108378

-HMHA1chr19

1077856

+
intron-intronENST00000361757ENST00000591169SBNO2chr19

1108378

-HMHA1chr19

1077856

+
intron-intronENST00000361757ENST00000592335SBNO2chr19

1108378

-HMHA1chr19

1077856

+
intron-intronENST00000438103ENST00000590577SBNO2chr19

1108378

-HMHA1chr19

1077856

+
intron-intronENST00000438103ENST00000591169SBNO2chr19

1108378

-HMHA1chr19

1077856

+
intron-intronENST00000438103ENST00000592335SBNO2chr19

1108378

-HMHA1chr19

1077856

+
intron-intronENST00000587024ENST00000590577SBNO2chr19

1108378

-HMHA1chr19

1077856

+
intron-intronENST00000587024ENST00000591169SBNO2chr19

1108378

-HMHA1chr19

1077856

+
intron-intronENST00000587024ENST00000592335SBNO2chr19

1108378

-HMHA1chr19

1077856

+

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)

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

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Fusion Genomic Features for SBNO2-HMHA1


check buttonFusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)
SBNO2chr191116019-HMHA1chr191080462+0.000328960.9996711
SBNO2chr191116019-HMHA1chr191080462+0.000328960.9996711
SBNO2chr191116019-HMHA1chr191080462+0.000328960.9996711
SBNO2chr191116019-HMHA1chr191080462+0.000328960.9996711

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.
genomic feature

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.
genomic feature of top 1%

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Fusion Protein Features for SBNO2-HMHA1


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/chr19:1116020/chr19:1080463)
- 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
..
FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.

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.
- In-frame and retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneSBNO2chr19:1116020chr19:1080463ENST00000361757-1732183_1956281367.0Compositional biasNote=Poly-Glu
HgeneSBNO2chr19:1116020chr19:1080463ENST00000438103-1429183_1955711310.0Compositional biasNote=Poly-Glu
TgeneHMHA1chr19:1116020chr19:1080463ENST000003130931323761_9746091137.0DomainRho-GAP
TgeneHMHA1chr19:1116020chr19:1080463ENST000005392431323761_9746251153.0DomainRho-GAP
TgeneHMHA1chr19:1116020chr19:1080463ENST000003130931323702_7476091137.0Zinc fingerPhorbol-ester/DAG-type
TgeneHMHA1chr19:1116020chr19:1080463ENST000005392431323702_7476251153.0Zinc fingerPhorbol-ester/DAG-type

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneSBNO2chr19:1116020chr19:1080463ENST00000361757-17321234_12946281367.0Compositional biasNote=Pro-rich
HgeneSBNO2chr19:1116020chr19:1080463ENST00000438103-14291234_12945711310.0Compositional biasNote=Pro-rich
TgeneHMHA1chr19:1116020chr19:1080463ENST000003130931323376_4126091137.0Coiled coilOntology_term=ECO:0000255
TgeneHMHA1chr19:1116020chr19:1080463ENST000003130931323440_4996091137.0Coiled coilOntology_term=ECO:0000255
TgeneHMHA1chr19:1116020chr19:1080463ENST000005392431323376_4126251153.0Coiled coilOntology_term=ECO:0000255
TgeneHMHA1chr19:1116020chr19:1080463ENST000005392431323440_4996251153.0Coiled coilOntology_term=ECO:0000255
TgeneHMHA1chr19:1116020chr19:1080463ENST000003130931323269_5396091137.0DomainF-BAR
TgeneHMHA1chr19:1116020chr19:1080463ENST000005392431323269_5396251153.0DomainF-BAR


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Fusion Gene Sequence for SBNO2-HMHA1


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.

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Fusion Gene PPI Analysis for SBNO2-HMHA1


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 (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs for SBNO2-HMHA1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for SBNO2-HMHA1


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