Home

Download

Statistics

Examples

Help

Contact

	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:RABGAP1L-KLHL20 (FusionGDB2 ID:71553)

Fusion Gene Summary for RABGAP1L-KLHL20

Fusion gene summary

Fusion gene information	Fusion gene name: RABGAP1L-KLHL20
	Fusion gene ID: 71553
		Hgene	Tgene
	Gene symbol	RABGAP1L	KLHL20
	Gene ID	9910	27252
	Gene name	RAB GTPase activating protein 1 like	kelch like family member 20
	Synonyms	HHL\|TBC1D18	KHLHX\|KLEIP\|KLHLX
	Cytomap	1q25.1	1q25.1
	Type of gene	protein-coding	protein-coding
	Description	rab GTPase-activating protein 1-likeTBC1 domain family, member 18expressed in hematopoietic cells, heart, liver (HLL)	kelch-like protein 20Kelch motif containing proteinkelch-like ECT2-interacting proteinkelch-like protein X
	Modification date	20200313	20200327
	UniProtAcc	.	Q9Y2M5
	Ensembl transtripts involved in fusion gene	ENST00000251507, ENST00000357444, ENST00000367689, ENST00000325589, ENST00000347255, ENST00000367686, ENST00000367687, ENST00000367688, ENST00000392064, ENST00000478442, ENST00000486220, ENST00000489615,	ENST00000493170, ENST00000209884, ENST00000546011,
Fusion gene scores	* DoF score	27 X 24 X 9=5832	5 X 6 X 5=150
	# samples	32	6
	** MAII score	log2(32/5832*10)=-4.18784690943957 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(6/150*10)=-1.32192809488736 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context	PubMed: RABGAP1L [Title/Abstract] AND KLHL20 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint	RABGAP1L(174128795)-KLHL20(173702852), # samples:1 RABGAP1L(174274265)-KLHL20(173735285), # 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
Hgene	RABGAP1L	GO:0032880	regulation of protein localization	16923123
Tgene	KLHL20	GO:0016567	protein ubiquitination	20389280
Tgene	KLHL20	GO:0043161	proteasome-mediated ubiquitin-dependent protein catabolic process	20389280
Tgene	KLHL20	GO:1990390	protein K33-linked ubiquitination	24768539

Fusion gene breakpoints across RABGAP1L (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 KLHL20 (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	HNSC	TCGA-CN-5361-01A	RABGAP1L	chr1	174128795	-	KLHL20	chr1	173702852	+
ChimerDB4	PRAD	TCGA-M7-A725-01A	RABGAP1L	chr1	174274265	-	KLHL20	chr1	173735285	+

Top

Fusion Gene ORF analysis for RABGAP1L-KLHL20

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	ENST00000251507	ENST00000493170	RABGAP1L	chr1	174274265	-	KLHL20	chr1	173735285	+
5CDS-intron	ENST00000357444	ENST00000493170	RABGAP1L	chr1	174274265	-	KLHL20	chr1	173735285	+
5CDS-intron	ENST00000367689	ENST00000493170	RABGAP1L	chr1	174274265	-	KLHL20	chr1	173735285	+
5UTR-3UTR	ENST00000251507	ENST00000493170	RABGAP1L	chr1	174128795	-	KLHL20	chr1	173702852	+
5UTR-3UTR	ENST00000357444	ENST00000493170	RABGAP1L	chr1	174128795	-	KLHL20	chr1	173702852	+
5UTR-3UTR	ENST00000367689	ENST00000493170	RABGAP1L	chr1	174128795	-	KLHL20	chr1	173702852	+
5UTR-intron	ENST00000251507	ENST00000209884	RABGAP1L	chr1	174128795	-	KLHL20	chr1	173702852	+
5UTR-intron	ENST00000251507	ENST00000546011	RABGAP1L	chr1	174128795	-	KLHL20	chr1	173702852	+
5UTR-intron	ENST00000357444	ENST00000209884	RABGAP1L	chr1	174128795	-	KLHL20	chr1	173702852	+
5UTR-intron	ENST00000357444	ENST00000546011	RABGAP1L	chr1	174128795	-	KLHL20	chr1	173702852	+
5UTR-intron	ENST00000367689	ENST00000209884	RABGAP1L	chr1	174128795	-	KLHL20	chr1	173702852	+
5UTR-intron	ENST00000367689	ENST00000546011	RABGAP1L	chr1	174128795	-	KLHL20	chr1	173702852	+
Frame-shift	ENST00000251507	ENST00000209884	RABGAP1L	chr1	174274265	-	KLHL20	chr1	173735285	+
Frame-shift	ENST00000251507	ENST00000546011	RABGAP1L	chr1	174274265	-	KLHL20	chr1	173735285	+
Frame-shift	ENST00000357444	ENST00000209884	RABGAP1L	chr1	174274265	-	KLHL20	chr1	173735285	+
Frame-shift	ENST00000357444	ENST00000546011	RABGAP1L	chr1	174274265	-	KLHL20	chr1	173735285	+
Frame-shift	ENST00000367689	ENST00000209884	RABGAP1L	chr1	174274265	-	KLHL20	chr1	173735285	+
Frame-shift	ENST00000367689	ENST00000546011	RABGAP1L	chr1	174274265	-	KLHL20	chr1	173735285	+
intron-3CDS	ENST00000325589	ENST00000209884	RABGAP1L	chr1	174274265	-	KLHL20	chr1	173735285	+
intron-3CDS	ENST00000325589	ENST00000546011	RABGAP1L	chr1	174274265	-	KLHL20	chr1	173735285	+
intron-3CDS	ENST00000347255	ENST00000209884	RABGAP1L	chr1	174274265	-	KLHL20	chr1	173735285	+
intron-3CDS	ENST00000347255	ENST00000546011	RABGAP1L	chr1	174274265	-	KLHL20	chr1	173735285	+
intron-3CDS	ENST00000367686	ENST00000209884	RABGAP1L	chr1	174274265	-	KLHL20	chr1	173735285	+
intron-3CDS	ENST00000367686	ENST00000546011	RABGAP1L	chr1	174274265	-	KLHL20	chr1	173735285	+
intron-3CDS	ENST00000367687	ENST00000209884	RABGAP1L	chr1	174274265	-	KLHL20	chr1	173735285	+
intron-3CDS	ENST00000367687	ENST00000546011	RABGAP1L	chr1	174274265	-	KLHL20	chr1	173735285	+
intron-3CDS	ENST00000367688	ENST00000209884	RABGAP1L	chr1	174274265	-	KLHL20	chr1	173735285	+
intron-3CDS	ENST00000367688	ENST00000546011	RABGAP1L	chr1	174274265	-	KLHL20	chr1	173735285	+
intron-3CDS	ENST00000392064	ENST00000209884	RABGAP1L	chr1	174274265	-	KLHL20	chr1	173735285	+
intron-3CDS	ENST00000392064	ENST00000546011	RABGAP1L	chr1	174274265	-	KLHL20	chr1	173735285	+
intron-3CDS	ENST00000478442	ENST00000209884	RABGAP1L	chr1	174274265	-	KLHL20	chr1	173735285	+
intron-3CDS	ENST00000478442	ENST00000546011	RABGAP1L	chr1	174274265	-	KLHL20	chr1	173735285	+
intron-3CDS	ENST00000486220	ENST00000209884	RABGAP1L	chr1	174274265	-	KLHL20	chr1	173735285	+
intron-3CDS	ENST00000486220	ENST00000546011	RABGAP1L	chr1	174274265	-	KLHL20	chr1	173735285	+
intron-3CDS	ENST00000489615	ENST00000209884	RABGAP1L	chr1	174274265	-	KLHL20	chr1	173735285	+
intron-3CDS	ENST00000489615	ENST00000546011	RABGAP1L	chr1	174274265	-	KLHL20	chr1	173735285	+
intron-3UTR	ENST00000325589	ENST00000493170	RABGAP1L	chr1	174128795	-	KLHL20	chr1	173702852	+
intron-3UTR	ENST00000347255	ENST00000493170	RABGAP1L	chr1	174128795	-	KLHL20	chr1	173702852	+
intron-3UTR	ENST00000367686	ENST00000493170	RABGAP1L	chr1	174128795	-	KLHL20	chr1	173702852	+
intron-3UTR	ENST00000367687	ENST00000493170	RABGAP1L	chr1	174128795	-	KLHL20	chr1	173702852	+
intron-3UTR	ENST00000367688	ENST00000493170	RABGAP1L	chr1	174128795	-	KLHL20	chr1	173702852	+
intron-3UTR	ENST00000392064	ENST00000493170	RABGAP1L	chr1	174128795	-	KLHL20	chr1	173702852	+
intron-3UTR	ENST00000478442	ENST00000493170	RABGAP1L	chr1	174128795	-	KLHL20	chr1	173702852	+
intron-3UTR	ENST00000486220	ENST00000493170	RABGAP1L	chr1	174128795	-	KLHL20	chr1	173702852	+
intron-3UTR	ENST00000489615	ENST00000493170	RABGAP1L	chr1	174128795	-	KLHL20	chr1	173702852	+
intron-intron	ENST00000325589	ENST00000209884	RABGAP1L	chr1	174128795	-	KLHL20	chr1	173702852	+
intron-intron	ENST00000325589	ENST00000493170	RABGAP1L	chr1	174274265	-	KLHL20	chr1	173735285	+
intron-intron	ENST00000325589	ENST00000546011	RABGAP1L	chr1	174128795	-	KLHL20	chr1	173702852	+
intron-intron	ENST00000347255	ENST00000209884	RABGAP1L	chr1	174128795	-	KLHL20	chr1	173702852	+
intron-intron	ENST00000347255	ENST00000493170	RABGAP1L	chr1	174274265	-	KLHL20	chr1	173735285	+
intron-intron	ENST00000347255	ENST00000546011	RABGAP1L	chr1	174128795	-	KLHL20	chr1	173702852	+
intron-intron	ENST00000367686	ENST00000209884	RABGAP1L	chr1	174128795	-	KLHL20	chr1	173702852	+
intron-intron	ENST00000367686	ENST00000493170	RABGAP1L	chr1	174274265	-	KLHL20	chr1	173735285	+
intron-intron	ENST00000367686	ENST00000546011	RABGAP1L	chr1	174128795	-	KLHL20	chr1	173702852	+
intron-intron	ENST00000367687	ENST00000209884	RABGAP1L	chr1	174128795	-	KLHL20	chr1	173702852	+
intron-intron	ENST00000367687	ENST00000493170	RABGAP1L	chr1	174274265	-	KLHL20	chr1	173735285	+
intron-intron	ENST00000367687	ENST00000546011	RABGAP1L	chr1	174128795	-	KLHL20	chr1	173702852	+
intron-intron	ENST00000367688	ENST00000209884	RABGAP1L	chr1	174128795	-	KLHL20	chr1	173702852	+
intron-intron	ENST00000367688	ENST00000493170	RABGAP1L	chr1	174274265	-	KLHL20	chr1	173735285	+
intron-intron	ENST00000367688	ENST00000546011	RABGAP1L	chr1	174128795	-	KLHL20	chr1	173702852	+
intron-intron	ENST00000392064	ENST00000209884	RABGAP1L	chr1	174128795	-	KLHL20	chr1	173702852	+
intron-intron	ENST00000392064	ENST00000493170	RABGAP1L	chr1	174274265	-	KLHL20	chr1	173735285	+
intron-intron	ENST00000392064	ENST00000546011	RABGAP1L	chr1	174128795	-	KLHL20	chr1	173702852	+
intron-intron	ENST00000478442	ENST00000209884	RABGAP1L	chr1	174128795	-	KLHL20	chr1	173702852	+
intron-intron	ENST00000478442	ENST00000493170	RABGAP1L	chr1	174274265	-	KLHL20	chr1	173735285	+
intron-intron	ENST00000478442	ENST00000546011	RABGAP1L	chr1	174128795	-	KLHL20	chr1	173702852	+
intron-intron	ENST00000486220	ENST00000209884	RABGAP1L	chr1	174128795	-	KLHL20	chr1	173702852	+
intron-intron	ENST00000486220	ENST00000493170	RABGAP1L	chr1	174274265	-	KLHL20	chr1	173735285	+
intron-intron	ENST00000486220	ENST00000546011	RABGAP1L	chr1	174128795	-	KLHL20	chr1	173702852	+
intron-intron	ENST00000489615	ENST00000209884	RABGAP1L	chr1	174128795	-	KLHL20	chr1	173702852	+
intron-intron	ENST00000489615	ENST00000493170	RABGAP1L	chr1	174274265	-	KLHL20	chr1	173735285	+
intron-intron	ENST00000489615	ENST00000546011	RABGAP1L	chr1	174128795	-	KLHL20	chr1	173702852	+

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

Top

Fusion Genomic Features for RABGAP1L-KLHL20

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)

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.

Top

Fusion Protein Features for RABGAP1L-KLHL20

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:174128795/:173702852)
- 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
.	KLHL20 Q9Y2M5
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: Substrate-specific adapter of a BCR (BTB-CUL3-RBX1) E3 ubiquitin-protein ligase complex involved in interferon response and anterograde Golgi to endosome transport. The BCR(KLHL20) E3 ubiquitin ligase complex mediates the ubiquitination of DAPK1, leading to its degradation by the proteasome, thereby acting as a negative regulator of apoptosis (PubMed:20389280). The BCR(KLHL20) E3 ubiquitin ligase complex also specifically mediates 'Lys-33'-linked ubiquitination (PubMed:24768539). Involved in anterograde Golgi to endosome transport by mediating 'Lys-33'-linked ubiquitination of CORO7, promoting interaction between CORO7 and EPS15, thereby facilitating actin polymerization and post-Golgi trafficking (PubMed:24768539). Also acts as a regulator of endothelial migration during angiogenesis by controlling the activation of Rho GTPases. The BCR(KLHL20) E3 ubiquitin ligase complex acts as a regulator of neurite outgrowth by mediating ubiquitination and degradation of PDZ-RhoGEF/ARHGEF11 (PubMed:21670212). In case of tumor, the BCR(KLHL20) E3 ubiquitin ligase complex is involved in tumor hypoxia: following hypoxia, the BCR(KLHL20)complex mediates ubiquitination and degradation of PML, potentiating HIF-1 signaling and cancer progression (PubMed:21840486). {ECO:0000269\|PubMed:14528312, ECO:0000269\|PubMed:17395875, ECO:0000269\|PubMed:20389280, ECO:0000269\|PubMed:21670212, ECO:0000269\|PubMed:21840486, ECO:0000269\|PubMed:24768539}.

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

- 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

Top

Fusion Gene Sequence for RABGAP1L-KLHL20

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.

Top

Fusion Gene PPI Analysis for RABGAP1L-KLHL20

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

- 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

Top

Related Drugs for RABGAP1L-KLHL20

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

Top

Related Diseases for RABGAP1L-KLHL20

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source