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	Fusion Gene Summary
	Fusion Gene ORF analysis
	Fusion Genomic Features
	Fusion Protein Features
	Fusion Gene Sequence
	Fusion Gene PPI analysis
	Related Drugs
	Related Diseases

Fusion gene:SNAPC1-HIF1A (FusionGDB2 ID:84429)

Fusion Gene Summary for SNAPC1-HIF1A

Fusion gene summary

Fusion gene information	Fusion gene name: SNAPC1-HIF1A
	Fusion gene ID: 84429
		Hgene	Tgene
	Gene symbol	SNAPC1	HIF1A
	Gene ID	6617	3091
	Gene name	small nuclear RNA activating complex polypeptide 1	hypoxia inducible factor 1 subunit alpha
	Synonyms	PTFgamma\|SNAP43	HIF-1-alpha\|HIF-1A\|HIF-1alpha\|HIF1\|HIF1-ALPHA\|MOP1\|PASD8\|bHLHe78
	Cytomap	14q23.2	14q23.2
	Type of gene	protein-coding	protein-coding
	Description	snRNA-activating protein complex subunit 1PSE-binding factor subunit gammaPTF subunit gammaSNAPc 43 kDa subunitSNAPc subunit 1proximal sequence element-binding transcription factor subunit gammasmall nuclear RNA activating complex, polypeptide 1, 43	hypoxia-inducible factor 1-alphaARNT interacting proteinPAS domain-containing protein 8basic-helix-loop-helix-PAS protein MOP1class E basic helix-loop-helix protein 78hypoxia inducible factor 1 alpha subunithypoxia inducible factor 1, alpha subunit
	Modification date	20200313	20200329
	UniProtAcc	.	Q9NWT6
	Ensembl transtripts involved in fusion gene	ENST00000216294,	ENST00000557206, ENST00000323441, ENST00000337138, ENST00000394997, ENST00000539097, ENST00000557538,
Fusion gene scores	* DoF score	4 X 4 X 4=64	7 X 7 X 3=147
	# samples	4	7
	** MAII score	log2(4/64*10)=-0.678071905112638 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(7/147*10)=-1.0703893278914 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context	PubMed: SNAPC1 [Title/Abstract] AND HIF1A [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint	SNAPC1(62249115)-HIF1A(62204805), # samples:1
Anticipated loss of major functional domain due to fusion event.

* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner	Gene	GO ID	GO term	PubMed ID
Tgene	HIF1A	GO:0001666	response to hypoxia	8756616\|9887100\|11782478\|15261140\|18419598
Tgene	HIF1A	GO:0006355	regulation of transcription, DNA-templated	11782478\|15261140
Tgene	HIF1A	GO:0010468	regulation of gene expression	18419598
Tgene	HIF1A	GO:0010573	vascular endothelial growth factor production	12958148
Tgene	HIF1A	GO:0010575	positive regulation of vascular endothelial growth factor production	8756616
Tgene	HIF1A	GO:0010628	positive regulation of gene expression	15459207\|24244340
Tgene	HIF1A	GO:0032364	oxygen homeostasis	16956324
Tgene	HIF1A	GO:0043619	regulation of transcription from RNA polymerase II promoter in response to oxidative stress	8089148\|8387214
Tgene	HIF1A	GO:0045893	positive regulation of transcription, DNA-templated	8089148\|9887100\|25043030
Tgene	HIF1A	GO:0045944	positive regulation of transcription by RNA polymerase II	11573933
Tgene	HIF1A	GO:0046886	positive regulation of hormone biosynthetic process	1448077
Tgene	HIF1A	GO:0061419	positive regulation of transcription from RNA polymerase II promoter in response to hypoxia	22735262
Tgene	HIF1A	GO:0071456	cellular response to hypoxia	11573933\|19528298\|20889502
Tgene	HIF1A	GO:1902895	positive regulation of pri-miRNA transcription by RNA polymerase II	19782034
Tgene	HIF1A	GO:1903377	negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway	24899725

Fusion gene breakpoints across SNAPC1 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Fusion gene breakpoints across HIF1A (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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.

Source	Disease	Sample	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
ChimerDB4	BRCA	TCGA-BH-A0C0-01A	SNAPC1	chr14	62249115	+	HIF1A	chr14	62204805	+

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Fusion Gene ORF analysis for SNAPC1-HIF1A

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.

ORF	Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
5CDS-intron	ENST00000216294	ENST00000557206	SNAPC1	chr14	62249115	+	HIF1A	chr14	62204805	+
In-frame	ENST00000216294	ENST00000323441	SNAPC1	chr14	62249115	+	HIF1A	chr14	62204805	+
In-frame	ENST00000216294	ENST00000337138	SNAPC1	chr14	62249115	+	HIF1A	chr14	62204805	+
In-frame	ENST00000216294	ENST00000394997	SNAPC1	chr14	62249115	+	HIF1A	chr14	62204805	+
In-frame	ENST00000216294	ENST00000539097	SNAPC1	chr14	62249115	+	HIF1A	chr14	62204805	+
In-frame	ENST00000216294	ENST00000557538	SNAPC1	chr14	62249115	+	HIF1A	chr14	62204805	+

ORFfinder result based on the fusion transcript sequence of in-frame fusion genes.

Henst

Tenst

Hgene

Hchr

Hbp

Hstrand

Tgene

Tchr

Tbp

Tstrand

Seq length
(transcript)

BP loci
(transcript)

Predicted start
(transcript)

Predicted stop
(transcript)

Seq length
(amino acids)

DeepORF 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.

Henst

Tenst

Hgene

Hchr

Hbp

Hstrand

Tgene

Tchr

Tbp

Tstrand

No-coding score

Coding score

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Fusion Genomic Features for SNAPC1-HIF1A

FusionAI 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.

Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	1-p	p (fusion gene breakpoint)
SNAPC1	chr14	62249115	+	HIF1A	chr14	62204804	+	1.50E-06	0.99999845
SNAPC1	chr14	62249115	+	HIF1A	chr14	62204804	+	1.50E-06	0.99999845

Distribution 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.

Distribution 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.

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Fusion Protein Features for SNAPC1-HIF1A

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr14:62249115/chr14:62204805)
- 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.

Main function of each fusion partner protein. (from UniProt)

Hgene	Tgene
.	HIF1A Q9NWT6
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: Hydroxylates HIF-1 alpha at 'Asn-803' in the C-terminal transactivation domain (CAD). Functions as an oxygen sensor and, under normoxic conditions, the hydroxylation prevents interaction of HIF-1 with transcriptional coactivators including Cbp/p300-interacting transactivator. Involved in transcriptional repression through interaction with HIF1A, VHL and histone deacetylases. Hydroxylates specific Asn residues within ankyrin repeat domains (ARD) of NFKB1, NFKBIA, NOTCH1, ASB4, PPP1R12A and several other ARD-containing proteins. Also hydroxylates Asp and His residues within ARDs of ANK1 and TNKS2, respectively. Negatively regulates NOTCH1 activity, accelerating myogenic differentiation. Positively regulates ASB4 activity, promoting vascular differentiation. {ECO:0000269\|PubMed:12042299, ECO:0000269\|PubMed:12080085, ECO:0000269\|PubMed:17003112, ECO:0000269\|PubMed:17573339, ECO:0000269\|PubMed:18299578, ECO:0000269\|PubMed:19245366, ECO:0000269\|PubMed:21177872, ECO:0000269\|PubMed:21251231}.

Retention 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.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

Hgene

SNAPC1

chr14:62249115

chr14:62204805

ENST00000216294

164_268

325

369.0

Region

Note=SNAPC4-binding

Hgene

SNAPC1

chr14:62249115

chr14:62204805

ENST00000216294

1_168

325

369.0

Region

Note=SNAPC3-binding

Tgene

HIF1A

chr14:62249115

chr14:62204805

ENST00000323441

615_621

416

736.0

Compositional bias

Note=Poly-Thr

Tgene

HIF1A

chr14:62249115

chr14:62204805

ENST00000337138

615_621

416

827.0

Compositional bias

Note=Poly-Thr

Tgene

HIF1A

chr14:62249115

chr14:62204805

ENST00000539097

615_621

440

851.0

Compositional bias

Note=Poly-Thr

Tgene

HIF1A

chr14:62249115

chr14:62204805

ENST00000323441

718_721

416

736.0

Motif

Nuclear localization signal

Tgene

HIF1A

chr14:62249115

chr14:62204805

ENST00000337138

718_721

416

827.0

Motif

Nuclear localization signal

Tgene

HIF1A

chr14:62249115

chr14:62204805

ENST00000539097

718_721

440

851.0

Motif

Nuclear localization signal

Tgene

HIF1A

chr14:62249115

chr14:62204805

ENST00000323441

531_575

416

736.0

Region

Note=NTAD

Tgene

HIF1A

chr14:62249115

chr14:62204805

ENST00000323441

556_572

416

736.0

Region

Note=C-terminal VHL recognition site

Tgene

HIF1A

chr14:62249115

chr14:62204805

ENST00000323441

576_785

416

736.0

Region

Note=ID

Tgene

HIF1A

chr14:62249115

chr14:62204805

ENST00000323441

786_826

416

736.0

Region

Note=CTAD

Tgene

HIF1A

chr14:62249115

chr14:62204805

ENST00000337138

531_575

416

827.0

Region

Note=NTAD

Tgene

HIF1A

chr14:62249115

chr14:62204805

ENST00000337138

556_572

416

827.0

Region

Note=C-terminal VHL recognition site

Tgene

HIF1A

chr14:62249115

chr14:62204805

ENST00000337138

576_785

416

827.0

Region

Note=ID

Tgene

HIF1A

chr14:62249115

chr14:62204805

ENST00000337138

786_826

416

827.0

Region

Note=CTAD

Tgene

HIF1A

chr14:62249115

chr14:62204805

ENST00000539097

531_575

440

851.0

Region

Note=NTAD

Tgene

HIF1A

chr14:62249115

chr14:62204805

ENST00000539097

556_572

440

851.0

Region

Note=C-terminal VHL recognition site

Tgene

HIF1A

chr14:62249115

chr14:62204805

ENST00000539097

576_785

440

851.0

Region

Note=ID

Tgene

HIF1A

chr14:62249115

chr14:62204805

ENST00000539097

786_826

440

851.0

Region

Note=CTAD

- In-frame and not-retained protein feature among the 13 regional features.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

Hgene

SNAPC1

chr14:62249115

chr14:62204805

ENST00000216294

347_352

325

369.0

Compositional bias

Note=Poly-Glu

Tgene

HIF1A

chr14:62249115

chr14:62204805

ENST00000323441

17_70

416

736.0

Domain

bHLH

Tgene

HIF1A

chr14:62249115

chr14:62204805

ENST00000323441

228_298

416

736.0

Domain

PAS 2

Tgene

HIF1A

chr14:62249115

chr14:62204805

ENST00000323441

302_345

416

736.0

Domain

Note=PAC

Tgene

HIF1A

chr14:62249115

chr14:62204805

ENST00000323441

85_158

416

736.0

Domain

PAS 1

Tgene

HIF1A

chr14:62249115

chr14:62204805

ENST00000337138

17_70

416

827.0

Domain

bHLH

Tgene

HIF1A

chr14:62249115

chr14:62204805

ENST00000337138

228_298

416

827.0

Domain

PAS 2

Tgene

HIF1A

chr14:62249115

chr14:62204805

ENST00000337138

302_345

416

827.0

Domain

Note=PAC

Tgene

HIF1A

chr14:62249115

chr14:62204805

ENST00000337138

85_158

416

827.0

Domain

PAS 1

Tgene

HIF1A

chr14:62249115

chr14:62204805

ENST00000539097

17_70

440

851.0

Domain

bHLH

Tgene

HIF1A

chr14:62249115

chr14:62204805

ENST00000539097

228_298

440

851.0

Domain

PAS 2

Tgene

HIF1A

chr14:62249115

chr14:62204805

ENST00000539097

302_345

440

851.0

Domain

Note=PAC

Tgene

HIF1A

chr14:62249115

chr14:62204805

ENST00000539097

85_158

440

851.0

Domain

PAS 1

Tgene

HIF1A

chr14:62249115

chr14:62204805

ENST00000323441

170_191

416

736.0

Region

Required for heterodimer formation with ARNT

Tgene

HIF1A

chr14:62249115

chr14:62204805

ENST00000323441

21_30

416

736.0

Region

DNA-binding

Tgene

HIF1A

chr14:62249115

chr14:62204805

ENST00000323441

380_417

416

736.0

Region

Note=N-terminal VHL recognition site

Tgene

HIF1A

chr14:62249115

chr14:62204805

ENST00000323441

401_603

416

736.0

Region

Note=ODD

Tgene

HIF1A

chr14:62249115

chr14:62204805

ENST00000337138

170_191

416

827.0

Region

Required for heterodimer formation with ARNT

Tgene

HIF1A

chr14:62249115

chr14:62204805

ENST00000337138

21_30

416

827.0

Region

DNA-binding

Tgene

HIF1A

chr14:62249115

chr14:62204805

ENST00000337138

380_417

416

827.0

Region

Note=N-terminal VHL recognition site

Tgene

HIF1A

chr14:62249115

chr14:62204805

ENST00000337138

401_603

416

827.0

Region

Note=ODD

Tgene

HIF1A

chr14:62249115

chr14:62204805

ENST00000539097

170_191

440

851.0

Region

Required for heterodimer formation with ARNT

Tgene

HIF1A

chr14:62249115

chr14:62204805

ENST00000539097

21_30

440

851.0

Region

DNA-binding

Tgene

HIF1A

chr14:62249115

chr14:62204805

ENST00000539097

380_417

440

851.0

Region

Note=N-terminal VHL recognition site

Tgene

HIF1A

chr14:62249115

chr14:62204805

ENST00000539097

401_603

440

851.0

Region

Note=ODD

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Fusion Gene Sequence for SNAPC1-HIF1A

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 SNAPC1-HIF1A

Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in
ChiPPI page.

Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)

Hgene

Hgene's interactors

Tgene

Tgene's interactors

- Retained PPIs in in-frame fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Still interaction with

- Lost PPIs in in-frame fusion.

Partner	Gene	Hbp	Tbp	ENST	Strand	BPexon	TotalExon	Protein feature loci	*BPloci	TotalLen	Interaction lost with
Tgene	HIF1A	chr14:62249115	chr14:62204805	ENST00000323441		8	14	1_401	416.3333333333333	736.0	TSGA10
Tgene	HIF1A	chr14:62249115	chr14:62204805	ENST00000337138		8	15	1_401	416.3333333333333	827.0	TSGA10
Tgene	HIF1A	chr14:62249115	chr14:62204805	ENST00000539097		8	15	1_401	440.3333333333333	851.0	TSGA10

- Retained PPIs, but lost function due to frame-shift fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

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Related Drugs for SNAPC1-HIF1A

Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)

Partner

Gene

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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Related Diseases for SNAPC1-HIF1A

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source