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Center for Computational Systems Medicine
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FusionGeneSummary

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FusionProtFeature

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FusionGeneSequence

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FusionGenePPI

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RelatedDrugs

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RelatedDiseases

Fusion gene ID: 34424

FusionGeneSummary for SLC38A9_KCNIP1

check button Fusion gene summary
Fusion gene informationFusion gene name: SLC38A9_KCNIP1
Fusion gene ID: 34424
HgeneTgene
Gene symbol

SLC38A9

KCNIP1

Gene ID

153129

30820

Gene namesolute carrier family 38 member 9potassium voltage-gated channel interacting protein 1
SynonymsURLC11KCHIP1|VABP
Cytomap

5q11.2

5q35.1

Type of geneprotein-codingprotein-coding
Descriptionsodium-coupled neutral amino acid transporter 9putative sodium-coupled neutral amino acid transporter 9up-regulated in lung cancer 11Kv channel-interacting protein 1A-type potassium channel modulatory protein 1Kv channel interacting protein 1potassium channel interacting protein 1vesicle APC-binding protein
Modification date2018052320180522
UniProtAcc

Q8NBW4

Q9NZI2

Ensembl transtripts involved in fusion geneENST00000504880, ENST00000396865, 
ENST00000539768, ENST00000318672, 
ENST00000515629, ENST00000416547, 
ENST00000512595, 		ENST00000518527, 
ENST00000377360, ENST00000328939, 
ENST00000390656, ENST00000520740, 
ENST00000434108, ENST00000411494, 
Fusion gene scores* DoF score1 X 1 X 1=17 X 7 X 5=245
# samples 110
** MAII scorelog2(1/1*10)=3.32192809488736log2(10/245*10)=-1.29278174922785
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: SLC38A9 [Title/Abstract] AND KCNIP1 [Title/Abstract] AND fusion [Title/Abstract]

Functional or gene categories assigned by FusionGDB annotation
* 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
HgeneSLC38A9

GO:0003333

amino acid transmembrane transport

25567906

HgeneSLC38A9

GO:0032008

positive regulation of TOR signaling

25561175|25567906

HgeneSLC38A9

GO:0071230

cellular response to amino acid stimulus

25561175|25567906

TgeneKCNIP1

GO:1901379

regulation of potassium ion transmembrane transport

10676964|17187064


check button Fusion gene information from three resources
(ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018))
* 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.
Data typeSourceCancer typeSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
TCGARVLUADTCGA-MN-A4N5-01ASLC38A9chr5

54945035

-KCNIP1chr5

170159804

+
* LD: Li Ding group's fusion gene list
  RV: Roel Verhaak group's fusion gene list
  ChiTaRs fusion database

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
intron-intronENST00000504880ENST00000518527SLC38A9chr5

54945035

-KCNIP1chr5

170159804

+
intron-intronENST00000504880ENST00000377360SLC38A9chr5

54945035

-KCNIP1chr5

170159804

+
intron-intronENST00000504880ENST00000328939SLC38A9chr5

54945035

-KCNIP1chr5

170159804

+
intron-intronENST00000504880ENST00000390656SLC38A9chr5

54945035

-KCNIP1chr5

170159804

+
intron-intronENST00000504880ENST00000520740SLC38A9chr5

54945035

-KCNIP1chr5

170159804

+
intron-intronENST00000504880ENST00000434108SLC38A9chr5

54945035

-KCNIP1chr5

170159804

+
intron-intronENST00000504880ENST00000411494SLC38A9chr5

54945035

-KCNIP1chr5

170159804

+
5CDS-intronENST00000396865ENST00000518527SLC38A9chr5

54945035

-KCNIP1chr5

170159804

+
5CDS-intronENST00000396865ENST00000377360SLC38A9chr5

54945035

-KCNIP1chr5

170159804

+
5CDS-intronENST00000396865ENST00000328939SLC38A9chr5

54945035

-KCNIP1chr5

170159804

+
5CDS-intronENST00000396865ENST00000390656SLC38A9chr5

54945035

-KCNIP1chr5

170159804

+
5CDS-intronENST00000396865ENST00000520740SLC38A9chr5

54945035

-KCNIP1chr5

170159804

+
5CDS-intronENST00000396865ENST00000434108SLC38A9chr5

54945035

-KCNIP1chr5

170159804

+
5CDS-intronENST00000396865ENST00000411494SLC38A9chr5

54945035

-KCNIP1chr5

170159804

+
5CDS-intronENST00000539768ENST00000518527SLC38A9chr5

54945035

-KCNIP1chr5

170159804

+
5CDS-intronENST00000539768ENST00000377360SLC38A9chr5

54945035

-KCNIP1chr5

170159804

+
5CDS-intronENST00000539768ENST00000328939SLC38A9chr5

54945035

-KCNIP1chr5

170159804

+
5CDS-intronENST00000539768ENST00000390656SLC38A9chr5

54945035

-KCNIP1chr5

170159804

+
5CDS-intronENST00000539768ENST00000520740SLC38A9chr5

54945035

-KCNIP1chr5

170159804

+
5CDS-intronENST00000539768ENST00000434108SLC38A9chr5

54945035

-KCNIP1chr5

170159804

+
5CDS-intronENST00000539768ENST00000411494SLC38A9chr5

54945035

-KCNIP1chr5

170159804

+
5CDS-intronENST00000318672ENST00000518527SLC38A9chr5

54945035

-KCNIP1chr5

170159804

+
5CDS-intronENST00000318672ENST00000377360SLC38A9chr5

54945035

-KCNIP1chr5

170159804

+
5CDS-intronENST00000318672ENST00000328939SLC38A9chr5

54945035

-KCNIP1chr5

170159804

+
5CDS-intronENST00000318672ENST00000390656SLC38A9chr5

54945035

-KCNIP1chr5

170159804

+
5CDS-intronENST00000318672ENST00000520740SLC38A9chr5

54945035

-KCNIP1chr5

170159804

+
5CDS-intronENST00000318672ENST00000434108SLC38A9chr5

54945035

-KCNIP1chr5

170159804

+
5CDS-intronENST00000318672ENST00000411494SLC38A9chr5

54945035

-KCNIP1chr5

170159804

+
5CDS-intronENST00000515629ENST00000518527SLC38A9chr5

54945035

-KCNIP1chr5

170159804

+
5CDS-intronENST00000515629ENST00000377360SLC38A9chr5

54945035

-KCNIP1chr5

170159804

+
5CDS-intronENST00000515629ENST00000328939SLC38A9chr5

54945035

-KCNIP1chr5

170159804

+
5CDS-intronENST00000515629ENST00000390656SLC38A9chr5

54945035

-KCNIP1chr5

170159804

+
5CDS-intronENST00000515629ENST00000520740SLC38A9chr5

54945035

-KCNIP1chr5

170159804

+
5CDS-intronENST00000515629ENST00000434108SLC38A9chr5

54945035

-KCNIP1chr5

170159804

+
5CDS-intronENST00000515629ENST00000411494SLC38A9chr5

54945035

-KCNIP1chr5

170159804

+
5CDS-intronENST00000416547ENST00000518527SLC38A9chr5

54945035

-KCNIP1chr5

170159804

+
5CDS-intronENST00000416547ENST00000377360SLC38A9chr5

54945035

-KCNIP1chr5

170159804

+
5CDS-intronENST00000416547ENST00000328939SLC38A9chr5

54945035

-KCNIP1chr5

170159804

+
5CDS-intronENST00000416547ENST00000390656SLC38A9chr5

54945035

-KCNIP1chr5

170159804

+
5CDS-intronENST00000416547ENST00000520740SLC38A9chr5

54945035

-KCNIP1chr5

170159804

+
5CDS-intronENST00000416547ENST00000434108SLC38A9chr5

54945035

-KCNIP1chr5

170159804

+
5CDS-intronENST00000416547ENST00000411494SLC38A9chr5

54945035

-KCNIP1chr5

170159804

+
intron-intronENST00000512595ENST00000518527SLC38A9chr5

54945035

-KCNIP1chr5

170159804

+
intron-intronENST00000512595ENST00000377360SLC38A9chr5

54945035

-KCNIP1chr5

170159804

+
intron-intronENST00000512595ENST00000328939SLC38A9chr5

54945035

-KCNIP1chr5

170159804

+
intron-intronENST00000512595ENST00000390656SLC38A9chr5

54945035

-KCNIP1chr5

170159804

+
intron-intronENST00000512595ENST00000520740SLC38A9chr5

54945035

-KCNIP1chr5

170159804

+
intron-intronENST00000512595ENST00000434108SLC38A9chr5

54945035

-KCNIP1chr5

170159804

+
intron-intronENST00000512595ENST00000411494SLC38A9chr5

54945035

-KCNIP1chr5

170159804

+

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FusionProtFeatures for SLC38A9_KCNIP1


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
SLC38A9

Q8NBW4

KCNIP1

Q9NZI2

Lysosomal amino acid transporter involved in theactivation of mTORC1 in response to amino acids. Probably acts asan amino acid sensor of the Rag GTPases and Ragulator complexes, 2complexes involved in amino acid sensing and activation of mTORC1,a signaling complex promoting cell growth in response to growthfactors, energy levels, and amino acids (PubMed:25561175,PubMed:25567906). Following activation by amino acids, theRagulator and Rag GTPases function as a scaffold recruiting mTORC1to lysosomes where it is in turn activated. SLC38A9 mediatestransport of amino acids with low capacity and specificity with aslight preference for polar amino acids, suggesting that it actsas an amino acid sensor instead (PubMed:25561175,PubMed:25567906). The high concentration of arginine in lysosomessuggests that it acts as an arginine sensor (PubMed:25567906).{ECO:0000269|PubMed:25561175, ECO:0000269|PubMed:25567906}. Regulatory subunit of Kv4/D (Shal)-type voltage-gatedrapidly inactivating A-type potassium channels. Regulates channeldensity, inactivation kinetics and rate of recovery frominactivation in a calcium-dependent and isoform-specific manner.In vitro, modulates KCND1/Kv4.1 and KCND2/Kv4.2 currents.Increases the presence of KCND2 at the cell surface.{ECO:0000269|PubMed:10676964, ECO:0000269|PubMed:11423117,ECO:0000269|PubMed:12829703, ECO:0000269|PubMed:17187064}.

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

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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FusionGeneSequence for SLC38A9_KCNIP1


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences.
(nt: nucleotides, aa: amino acids)

* Fusion amino acid sequences.

* Fusion transcript sequences (only coding sequence (CDS) region).

* Fusion transcript sequences (Full-length transcript).

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FusionGenePPI for SLC38A9_KCNIP1


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
SLC38A9HLA-DQA1, LGALS3, ASGR2, LGALS8, RRAGA, LGALS9, LGALS9C, HTR3C, TCTN3, FPR2, ATP2B2, RRAGB, LAMTOR1, LAMTOR2, LAMTOR4, LAMTOR5, RRAGC, ATP6V0D1, ATP6V1B2KCNIP1SPP1, KCND2, KCNIP2, KCNIP4, KCND3


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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RelatedDrugs for SLC38A9_KCNIP1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for SLC38A9_KCNIP1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneSLC38A9C0023903Liver neoplasms1CTD_human