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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:COL4A6-LAIR1 (FusionGDB2 ID:HG1288TG3903)

Fusion Gene Summary for COL4A6-LAIR1

check button Fusion gene summary
Fusion gene informationFusion gene name: COL4A6-LAIR1
Fusion gene ID: hg1288tg3903
HgeneTgene
Gene symbol

COL4A6

LAIR1

Gene ID

1288

3903

Gene namecollagen type IV alpha 6 chainleukocyte associated immunoglobulin like receptor 1
SynonymsCXDELq22.3|DELXq22.3|DFNX6CD305|LAIR-1
Cytomap('COL4A6')('LAIR1')

Xq22.3

19q13.42

Type of geneprotein-codingprotein-coding
Descriptioncollagen alpha-6(IV) chaincollagen IV, alpha-6 polypeptidecollagen of basement membrane, alpha-6collagen, type IV, alpha 6dJ889N15.4 (Collagen Alpha 6(IV))leukocyte-associated immunoglobulin-like receptor 1immunoglobulin heavy chain variable regionleukocyte-associated Ig-like receptor 1
Modification date2020031320200313
UniProtAcc

Q14031

.
Ensembl transtripts involved in fusion geneENST00000334504, ENST00000372216, 
ENST00000394872, ENST00000418180, 
ENST00000461897, ENST00000538570, 
ENST00000545689, 
Fusion gene scores* DoF score4 X 4 X 1=163 X 3 X 2=18
# samples 43
** MAII scorelog2(4/16*10)=1.32192809488736
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0		log2(3/18*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: COL4A6 [Title/Abstract] AND LAIR1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCOL4A6(107618926)-LAIR1(54866177), # 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)

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


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
ChiTaRS5.0N/AAA533135COL4A6chrX

107618926

+LAIR1chr19

54866177

+


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Fusion Gene ORF analysis for COL4A6-LAIR1

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-3UTRENST00000334504ENST00000391743COL4A6chrX

107618926

+LAIR1chr19

54866177

+
intron-3UTRENST00000372216ENST00000391743COL4A6chrX

107618926

+LAIR1chr19

54866177

+
intron-3UTRENST00000394872ENST00000391743COL4A6chrX

107618926

+LAIR1chr19

54866177

+
intron-3UTRENST00000418180ENST00000391743COL4A6chrX

107618926

+LAIR1chr19

54866177

+
intron-3UTRENST00000461897ENST00000391743COL4A6chrX

107618926

+LAIR1chr19

54866177

+
intron-3UTRENST00000538570ENST00000391743COL4A6chrX

107618926

+LAIR1chr19

54866177

+
intron-3UTRENST00000545689ENST00000391743COL4A6chrX

107618926

+LAIR1chr19

54866177

+
intron-intronENST00000334504ENST00000313038COL4A6chrX

107618926

+LAIR1chr19

54866177

+
intron-intronENST00000334504ENST00000348231COL4A6chrX

107618926

+LAIR1chr19

54866177

+
intron-intronENST00000334504ENST00000391742COL4A6chrX

107618926

+LAIR1chr19

54866177

+
intron-intronENST00000334504ENST00000434277COL4A6chrX

107618926

+LAIR1chr19

54866177

+
intron-intronENST00000334504ENST00000463489COL4A6chrX

107618926

+LAIR1chr19

54866177

+
intron-intronENST00000334504ENST00000474878COL4A6chrX

107618926

+LAIR1chr19

54866177

+
intron-intronENST00000372216ENST00000313038COL4A6chrX

107618926

+LAIR1chr19

54866177

+
intron-intronENST00000372216ENST00000348231COL4A6chrX

107618926

+LAIR1chr19

54866177

+
intron-intronENST00000372216ENST00000391742COL4A6chrX

107618926

+LAIR1chr19

54866177

+
intron-intronENST00000372216ENST00000434277COL4A6chrX

107618926

+LAIR1chr19

54866177

+
intron-intronENST00000372216ENST00000463489COL4A6chrX

107618926

+LAIR1chr19

54866177

+
intron-intronENST00000372216ENST00000474878COL4A6chrX

107618926

+LAIR1chr19

54866177

+
intron-intronENST00000394872ENST00000313038COL4A6chrX

107618926

+LAIR1chr19

54866177

+
intron-intronENST00000394872ENST00000348231COL4A6chrX

107618926

+LAIR1chr19

54866177

+
intron-intronENST00000394872ENST00000391742COL4A6chrX

107618926

+LAIR1chr19

54866177

+
intron-intronENST00000394872ENST00000434277COL4A6chrX

107618926

+LAIR1chr19

54866177

+
intron-intronENST00000394872ENST00000463489COL4A6chrX

107618926

+LAIR1chr19

54866177

+
intron-intronENST00000394872ENST00000474878COL4A6chrX

107618926

+LAIR1chr19

54866177

+
intron-intronENST00000418180ENST00000313038COL4A6chrX

107618926

+LAIR1chr19

54866177

+
intron-intronENST00000418180ENST00000348231COL4A6chrX

107618926

+LAIR1chr19

54866177

+
intron-intronENST00000418180ENST00000391742COL4A6chrX

107618926

+LAIR1chr19

54866177

+
intron-intronENST00000418180ENST00000434277COL4A6chrX

107618926

+LAIR1chr19

54866177

+
intron-intronENST00000418180ENST00000463489COL4A6chrX

107618926

+LAIR1chr19

54866177

+
intron-intronENST00000418180ENST00000474878COL4A6chrX

107618926

+LAIR1chr19

54866177

+
intron-intronENST00000461897ENST00000313038COL4A6chrX

107618926

+LAIR1chr19

54866177

+
intron-intronENST00000461897ENST00000348231COL4A6chrX

107618926

+LAIR1chr19

54866177

+
intron-intronENST00000461897ENST00000391742COL4A6chrX

107618926

+LAIR1chr19

54866177

+
intron-intronENST00000461897ENST00000434277COL4A6chrX

107618926

+LAIR1chr19

54866177

+
intron-intronENST00000461897ENST00000463489COL4A6chrX

107618926

+LAIR1chr19

54866177

+
intron-intronENST00000461897ENST00000474878COL4A6chrX

107618926

+LAIR1chr19

54866177

+
intron-intronENST00000538570ENST00000313038COL4A6chrX

107618926

+LAIR1chr19

54866177

+
intron-intronENST00000538570ENST00000348231COL4A6chrX

107618926

+LAIR1chr19

54866177

+
intron-intronENST00000538570ENST00000391742COL4A6chrX

107618926

+LAIR1chr19

54866177

+
intron-intronENST00000538570ENST00000434277COL4A6chrX

107618926

+LAIR1chr19

54866177

+
intron-intronENST00000538570ENST00000463489COL4A6chrX

107618926

+LAIR1chr19

54866177

+
intron-intronENST00000538570ENST00000474878COL4A6chrX

107618926

+LAIR1chr19

54866177

+
intron-intronENST00000545689ENST00000313038COL4A6chrX

107618926

+LAIR1chr19

54866177

+
intron-intronENST00000545689ENST00000348231COL4A6chrX

107618926

+LAIR1chr19

54866177

+
intron-intronENST00000545689ENST00000391742COL4A6chrX

107618926

+LAIR1chr19

54866177

+
intron-intronENST00000545689ENST00000434277COL4A6chrX

107618926

+LAIR1chr19

54866177

+
intron-intronENST00000545689ENST00000463489COL4A6chrX

107618926

+LAIR1chr19

54866177

+
intron-intronENST00000545689ENST00000474878COL4A6chrX

107618926

+LAIR1chr19

54866177

+

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 COL4A6-LAIR1


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)


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Fusion Protein Features for COL4A6-LAIR1


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/:107618926/:54866177)
- 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
COL4A6

Q14031

.
FUNCTION: Type IV collagen is the major structural component of glomerular basement membranes (GBM), forming a 'chicken-wire' meshwork together with laminins, proteoglycans and entactin/nidogen.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

- 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 COL4A6-LAIR1


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 COL4A6-LAIR1


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 COL4A6-LAIR1


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 COL4A6-LAIR1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCOL4A6C3806737DEAFNESS, X-LINKED 63CLINGEN;CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneCOL4A6C1839884Leiomyomatosis, esophageal and vulval, with nephropathy2GENOMICS_ENGLAND;ORPHANET
HgeneCOL4A6C0000786Spontaneous abortion1CTD_human
HgeneCOL4A6C0000822Abortion, Tubal1CTD_human
HgeneCOL4A6C0086533Leiomyoma, Epithelioid1CTD_human
HgeneCOL4A6C3830362Early Pregnancy Loss1CTD_human
HgeneCOL4A6C4552766Miscarriage1CTD_human
TgeneC0017661IGA Glomerulonephritis1CTD_human