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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:TCF4-LIPA (FusionGDB2 ID:89165)

Fusion Gene Summary for TCF4-LIPA

check button Fusion gene summary
Fusion gene informationFusion gene name: TCF4-LIPA
Fusion gene ID: 89165
HgeneTgene
Gene symbol

TCF4

LIPA

Gene ID

6934

10648

Gene nametranscription factor 7 like 2secretoglobin family 1D member 1
SynonymsTCF-4|TCF4LIPA|LPHA|LPNA
Cytomap

10q25.2-q25.3

11q12.3

Type of geneprotein-codingprotein-coding
Descriptiontranscription factor 7-like 2HMG box transcription factor 4T-cell factor 4T-cell-specific transcription factor 4hTCF-4transcription factor 7-like 2 (T-cell specific, HMG-box)secretoglobin family 1D member 1lipophilin A (uteroglobin family member)lipophilin-Aprostatein-like lipophilin A
Modification date2020031520200313
UniProtAcc.

LIPM

Ensembl transtripts involved in fusion geneENST00000354452, ENST00000356073, 
ENST00000568673, ENST00000457482, 
ENST00000543082, ENST00000540999, 
ENST00000537578, ENST00000564999, 
ENST00000568740, ENST00000537856, 
ENST00000544241, ENST00000561992, 
ENST00000561831, ENST00000565018, 
ENST00000570287, ENST00000564228, 
ENST00000567880, ENST00000566286, 
ENST00000566279, ENST00000564403, 
ENST00000398339, ENST00000570177, 
ENST00000563760, 		ENST00000371837, 
ENST00000487618, ENST00000336233, 
ENST00000456827, 
Fusion gene scores* DoF score13 X 13 X 4=6765 X 4 X 4=80
# samples 136
** MAII scorelog2(13/676*10)=-2.37851162325373
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(6/80*10)=-0.415037499278844
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: TCF4 [Title/Abstract] AND LIPA [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointTCF4(52891012)-LIPA(90975727), # 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
HgeneTCF4

GO:0000122

negative regulation of transcription by RNA polymerase II

12799378

HgeneTCF4

GO:0006357

regulation of transcription by RNA polymerase II

9727977

HgeneTCF4

GO:0032092

positive regulation of protein binding

12799378

HgeneTCF4

GO:0032350

regulation of hormone metabolic process

15525634

HgeneTCF4

GO:0042593

glucose homeostasis

15525634

HgeneTCF4

GO:0043433

negative regulation of DNA-binding transcription factor activity

12799378

HgeneTCF4

GO:0045444

fat cell differentiation

10937998

HgeneTCF4

GO:0045892

negative regulation of transcription, DNA-templated

12799378|15525634

HgeneTCF4

GO:0045944

positive regulation of transcription by RNA polymerase II

9065401|19168596

HgeneTCF4

GO:0048625

myoblast fate commitment

10937998


check buttonFusion gene breakpoints across TCF4 (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 LIPA (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
ChiTaRS5.0N/AAI265859TCF4chr18

52891012

+LIPAchr10

90975727

+


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Fusion Gene ORF analysis for TCF4-LIPA

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-3CDSENST00000354452ENST00000371837TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000354452ENST00000487618TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000354452ENST00000336233TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000354452ENST00000456827TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-3CDSENST00000356073ENST00000371837TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000356073ENST00000487618TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000356073ENST00000336233TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000356073ENST00000456827TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-3CDSENST00000568673ENST00000371837TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000568673ENST00000487618TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000568673ENST00000336233TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000568673ENST00000456827TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-3CDSENST00000457482ENST00000371837TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000457482ENST00000487618TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000457482ENST00000336233TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000457482ENST00000456827TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-3CDSENST00000543082ENST00000371837TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000543082ENST00000487618TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000543082ENST00000336233TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000543082ENST00000456827TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-3CDSENST00000540999ENST00000371837TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000540999ENST00000487618TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000540999ENST00000336233TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000540999ENST00000456827TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-3CDSENST00000537578ENST00000371837TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000537578ENST00000487618TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000537578ENST00000336233TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000537578ENST00000456827TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-3CDSENST00000564999ENST00000371837TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000564999ENST00000487618TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000564999ENST00000336233TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000564999ENST00000456827TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-3CDSENST00000568740ENST00000371837TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000568740ENST00000487618TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000568740ENST00000336233TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000568740ENST00000456827TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-3CDSENST00000537856ENST00000371837TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000537856ENST00000487618TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000537856ENST00000336233TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000537856ENST00000456827TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-3CDSENST00000544241ENST00000371837TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000544241ENST00000487618TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000544241ENST00000336233TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000544241ENST00000456827TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-3CDSENST00000561992ENST00000371837TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000561992ENST00000487618TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000561992ENST00000336233TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000561992ENST00000456827TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-3CDSENST00000561831ENST00000371837TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000561831ENST00000487618TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000561831ENST00000336233TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000561831ENST00000456827TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-3CDSENST00000565018ENST00000371837TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000565018ENST00000487618TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000565018ENST00000336233TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000565018ENST00000456827TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-3CDSENST00000570287ENST00000371837TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000570287ENST00000487618TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000570287ENST00000336233TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000570287ENST00000456827TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-3CDSENST00000564228ENST00000371837TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000564228ENST00000487618TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000564228ENST00000336233TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000564228ENST00000456827TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-3CDSENST00000567880ENST00000371837TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000567880ENST00000487618TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000567880ENST00000336233TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000567880ENST00000456827TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-3CDSENST00000566286ENST00000371837TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000566286ENST00000487618TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000566286ENST00000336233TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000566286ENST00000456827TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-3CDSENST00000566279ENST00000371837TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000566279ENST00000487618TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000566279ENST00000336233TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000566279ENST00000456827TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-3CDSENST00000564403ENST00000371837TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000564403ENST00000487618TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000564403ENST00000336233TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000564403ENST00000456827TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-3CDSENST00000398339ENST00000371837TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000398339ENST00000487618TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000398339ENST00000336233TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000398339ENST00000456827TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-3CDSENST00000570177ENST00000371837TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000570177ENST00000487618TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000570177ENST00000336233TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000570177ENST00000456827TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-3CDSENST00000563760ENST00000371837TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000563760ENST00000487618TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000563760ENST00000336233TCF4chr18

52891012

+LIPAchr10

90975727

+
intron-intronENST00000563760ENST00000456827TCF4chr18

52891012

+LIPAchr10

90975727

+

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 TCF4-LIPA


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)

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 TCF4-LIPA


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
.LIPA

LIPM

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.423

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 TCF4-LIPA


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 TCF4-LIPA


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 TCF4-LIPA


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 TCF4-LIPA


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneTCF4C1970431PITT-HOPKINS SYNDROME14CLINGEN;CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneTCF4C0005586Bipolar Disorder5PSYGENET
HgeneTCF4C0036341Schizophrenia4PSYGENET
HgeneTCF4C0016781Fuchs Endothelial Dystrophy1ORPHANET
HgeneTCF4C0018799Heart Diseases1CTD_human
HgeneTCF4C0022333Jacksonian Seizure1CTD_human
HgeneTCF4C0023893Liver Cirrhosis, Experimental1CTD_human
HgeneTCF4C0023903Liver neoplasms1CTD_human
HgeneTCF4C0025958Microcephaly1CTD_human
HgeneTCF4C0033975Psychotic Disorders1PSYGENET
HgeneTCF4C0036572Seizures1CTD_human
HgeneTCF4C0149958Complex partial seizures1CTD_human
HgeneTCF4C0234533Generalized seizures1CTD_human
HgeneTCF4C0234535Clonic Seizures1CTD_human
HgeneTCF4C0270824Visual seizure1CTD_human
HgeneTCF4C0270844Tonic Seizures1CTD_human
HgeneTCF4C0270846Epileptic drop attack1CTD_human
HgeneTCF4C0345904Malignant neoplasm of liver1CTD_human
HgeneTCF4C0349204Nonorganic psychosis1PSYGENET
HgeneTCF4C0376634Craniofacial Abnormalities1CTD_human
HgeneTCF4C0422850Seizures, Somatosensory1CTD_human
HgeneTCF4C0422852Seizures, Auditory1CTD_human
HgeneTCF4C0422853Olfactory seizure1CTD_human
HgeneTCF4C0422854Gustatory seizure1CTD_human
HgeneTCF4C0422855Vertiginous seizure1CTD_human
HgeneTCF4C0494475Tonic - clonic seizures1CTD_human
HgeneTCF4C0566602Primary sclerosing cholangitis1ORPHANET
HgeneTCF4C0751056Non-epileptic convulsion1CTD_human
HgeneTCF4C0751110Single Seizure1CTD_human
HgeneTCF4C0751123Atonic Absence Seizures1CTD_human
HgeneTCF4C0751494Convulsive Seizures1CTD_human
HgeneTCF4C0751495Seizures, Focal1CTD_human
HgeneTCF4C0751496Seizures, Sensory1CTD_human
HgeneTCF4C1456784Paranoia1PSYGENET
HgeneTCF4C1535926Neurodevelopmental Disorders1CTD_human
HgeneTCF4C1956147Microlissencephaly1CTD_human
HgeneTCF4C2750451CORNEAL DYSTROPHY, FUCHS ENDOTHELIAL, 31CTD_human;GENOMICS_ENGLAND
HgeneTCF4C2931456Prostate cancer, familial1CTD_human
HgeneTCF4C3495874Nonepileptic Seizures1CTD_human
HgeneTCF4C3853041Severe Congenital Microcephaly1CTD_human
HgeneTCF4C4048158Convulsions1CTD_human
HgeneTCF4C4316903Absence Seizures1CTD_human
HgeneTCF4C4317109Epileptic Seizures1CTD_human
HgeneTCF4C4317123Myoclonic Seizures1CTD_human
HgeneTCF4C4505436Generalized Absence Seizures1CTD_human
HgeneTCF4C4721453Peripheral Nervous System Diseases1CTD_human
HgeneTCF4C4722327PROSTATE CANCER, HEREDITARY, 11CTD_human
TgeneLIPAC0043208Wolman Disease6GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneLIPAC0008384Cholesterol Ester Storage Disease3CTD_human;GENOMICS_ENGLAND;ORPHANET
TgeneLIPAC2936797Acid cholesteryl ester hydrolase deficiency, type 22CTD_human;GENOMICS_ENGLAND
TgeneLIPAC0008370Cholestasis1GENOMICS_ENGLAND
TgeneLIPAC0010054Coronary Arteriosclerosis1CTD_human
TgeneLIPAC0020305Hydrops Fetalis1GENOMICS_ENGLAND
TgeneLIPAC0220756Niemann-Pick Disease, Type C1CTD_human
TgeneLIPAC0268247Niemann-Pick Disease, Type D1CTD_human
TgeneLIPAC1956346Coronary Artery Disease1CTD_human
TgeneLIPAC3179455Niemann-Pick Disease, Type C11CTD_human