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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:LPHN3-AMTN (FusionGDB2 ID:49279)

Fusion Gene Summary for LPHN3-AMTN

check button Fusion gene summary
Fusion gene informationFusion gene name: LPHN3-AMTN
Fusion gene ID: 49279
HgeneTgene
Gene symbol

LPHN3

AMTN

Gene ID

23284

401138

Gene nameadhesion G protein-coupled receptor L3amelotin
SynonymsCIRL3|CL3|LEC3|LPHN3AI3B|UNQ689
Cytomap

4q13.1

4q13.3

Type of geneprotein-codingprotein-coding
Descriptionadhesion G protein-coupled receptor L3CIRL-3calcium-independent alpha-latrotoxin receptor 3latrophilin homolog 3 (cow)latrophilin-3lectomedin 3amelotinRSTI689
Modification date2020031320200313
UniProtAcc.

Q6UX39

Ensembl transtripts involved in fusion geneENST00000512091, ENST00000514591, 
ENST00000511324, ENST00000506700, 
ENST00000509896, ENST00000545650, 
ENST00000508693, ENST00000507164, 
ENST00000507625, ENST00000514157, 
ENST00000504896, ENST00000514996, 
ENST00000506720, ENST00000506746, 
ENST00000508946, ENST00000508078, 
ENST00000339336, ENST00000504451, 
Fusion gene scores* DoF score6 X 4 X 4=964 X 4 X 3=48
# samples 74
** MAII scorelog2(7/96*10)=-0.45567948377619
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(4/48*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: LPHN3 [Title/Abstract] AND AMTN [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointLPHN3(62679607)-AMTN(71389585), # samples:2
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)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneLPHN3

GO:0098742

cell-cell adhesion via plasma-membrane adhesion molecules

26235030

TgeneAMTN

GO:0070169

positive regulation of biomineral tissue development

25407797


check buttonFusion gene breakpoints across LPHN3 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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

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
ChimerDB4KIRCTCGA-BP-5201-01ALPHN3chr4

62679607

+AMTNchr4

71389585

+
ChimerDB4KIRCTCGA-BP-5201-01ALPHN3chr4

62679607

-AMTNchr4

71389585

+


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Fusion Gene ORF analysis for LPHN3-AMTN

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
Frame-shiftENST00000512091ENST00000339336LPHN3chr4

62679607

+AMTNchr4

71389585

+
Frame-shiftENST00000512091ENST00000504451LPHN3chr4

62679607

+AMTNchr4

71389585

+
Frame-shiftENST00000514591ENST00000339336LPHN3chr4

62679607

+AMTNchr4

71389585

+
Frame-shiftENST00000514591ENST00000504451LPHN3chr4

62679607

+AMTNchr4

71389585

+
Frame-shiftENST00000511324ENST00000339336LPHN3chr4

62679607

+AMTNchr4

71389585

+
Frame-shiftENST00000511324ENST00000504451LPHN3chr4

62679607

+AMTNchr4

71389585

+
Frame-shiftENST00000506700ENST00000339336LPHN3chr4

62679607

+AMTNchr4

71389585

+
Frame-shiftENST00000506700ENST00000504451LPHN3chr4

62679607

+AMTNchr4

71389585

+
Frame-shiftENST00000509896ENST00000339336LPHN3chr4

62679607

+AMTNchr4

71389585

+
Frame-shiftENST00000509896ENST00000504451LPHN3chr4

62679607

+AMTNchr4

71389585

+
Frame-shiftENST00000545650ENST00000339336LPHN3chr4

62679607

+AMTNchr4

71389585

+
Frame-shiftENST00000545650ENST00000504451LPHN3chr4

62679607

+AMTNchr4

71389585

+
Frame-shiftENST00000508693ENST00000339336LPHN3chr4

62679607

+AMTNchr4

71389585

+
Frame-shiftENST00000508693ENST00000504451LPHN3chr4

62679607

+AMTNchr4

71389585

+
Frame-shiftENST00000507164ENST00000339336LPHN3chr4

62679607

+AMTNchr4

71389585

+
Frame-shiftENST00000507164ENST00000504451LPHN3chr4

62679607

+AMTNchr4

71389585

+
Frame-shiftENST00000507625ENST00000339336LPHN3chr4

62679607

+AMTNchr4

71389585

+
Frame-shiftENST00000507625ENST00000504451LPHN3chr4

62679607

+AMTNchr4

71389585

+
Frame-shiftENST00000514157ENST00000339336LPHN3chr4

62679607

+AMTNchr4

71389585

+
Frame-shiftENST00000514157ENST00000504451LPHN3chr4

62679607

+AMTNchr4

71389585

+
Frame-shiftENST00000504896ENST00000339336LPHN3chr4

62679607

+AMTNchr4

71389585

+
Frame-shiftENST00000504896ENST00000504451LPHN3chr4

62679607

+AMTNchr4

71389585

+
Frame-shiftENST00000514996ENST00000339336LPHN3chr4

62679607

+AMTNchr4

71389585

+
Frame-shiftENST00000514996ENST00000504451LPHN3chr4

62679607

+AMTNchr4

71389585

+
Frame-shiftENST00000506720ENST00000339336LPHN3chr4

62679607

+AMTNchr4

71389585

+
Frame-shiftENST00000506720ENST00000504451LPHN3chr4

62679607

+AMTNchr4

71389585

+
Frame-shiftENST00000506746ENST00000339336LPHN3chr4

62679607

+AMTNchr4

71389585

+
Frame-shiftENST00000506746ENST00000504451LPHN3chr4

62679607

+AMTNchr4

71389585

+
Frame-shiftENST00000508946ENST00000339336LPHN3chr4

62679607

+AMTNchr4

71389585

+
Frame-shiftENST00000508946ENST00000504451LPHN3chr4

62679607

+AMTNchr4

71389585

+
intron-3CDSENST00000508078ENST00000339336LPHN3chr4

62679607

+AMTNchr4

71389585

+
intron-3CDSENST00000508078ENST00000504451LPHN3chr4

62679607

+AMTNchr4

71389585

+

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 LPHN3-AMTN


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)
LPHN3chr462679607+AMTNchr471389584+0.0280831230.9719169
LPHN3chr462679607+AMTNchr471389584+0.0280831230.9719169

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.

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.

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Fusion Protein Features for LPHN3-AMTN


check button Go to

FGviewer for the breakpoints of :-:

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

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

Q6UX39

FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.FUNCTION: Is a promoter of calcium phosphate mineralization, playing a critical role in the formation of the compact, mineralized, aprismatic enamel surface layer during the maturation stage of amelogenesis. {ECO:0000269|PubMed:25407797}.

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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Fusion Gene Sequence for LPHN3-AMTN


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 LPHN3-AMTN


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 LPHN3-AMTN


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 LPHN3-AMTN


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneAMTNC0002452Amelogenesis Imperfecta1GENOMICS_ENGLAND
TgeneAMTNC0399372Amelogenesis Imperfecta hypomaturation type1GENOMICS_ENGLAND
TgeneAMTNC0399376Amelogenesis Imperfecta, Type III1ORPHANET
TgeneAMTNC4539891AMELOGENESIS IMPERFECTA, TYPE IIIB1GENOMICS_ENGLAND