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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: 20056

FusionGeneSummary for LRBA_CHCHD3

check button Fusion gene summary
Fusion gene informationFusion gene name: LRBA_CHCHD3
Fusion gene ID: 20056
HgeneTgene
Gene symbol

LRBA

CHCHD3

Gene ID

987

54927

Gene nameLPS responsive beige-like anchor proteincoiled-coil-helix-coiled-coil-helix domain containing 3
SynonymsBGL|CDC4L|CVID8|LAB300|LBAMINOS3|Mic19|PPP1R22
Cytomap

4q31.3

7q32.3-q33

Type of geneprotein-codingprotein-coding
Descriptionlipopolysaccharide-responsive and beige-like anchor proteinCDC4-like proteinLPS-responsive vesicle trafficking, beach and anchor containingvesicle trafficking, beach and anchor containingMICOS complex subunit MIC19coiled-coil-helix-coiled-coil-helix domain-containing protein 3, mitochondrialmitochondrial inner membrane organizing system 3protein phosphatase 1, regulatory subunit 22
Modification date2018051920180527
UniProtAcc

P50851

Q9NX63

Ensembl transtripts involved in fusion geneENST00000535741, ENST00000510413, 
ENST00000503716, ENST00000357115, 
ENST00000507224, 
ENST00000262570, 
ENST00000448878, ENST00000476546, 
ENST00000542753, 
Fusion gene scores* DoF score16 X 15 X 12=288011 X 13 X 4=572
# samples 2214
** MAII scorelog2(22/2880*10)=-3.71049338280502
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(14/572*10)=-2.03058831983342
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: LRBA [Title/Abstract] AND CHCHD3 [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
TgeneCHCHD3

GO:0000122

negative regulation of transcription by RNA polymerase II

22567091


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
TCGARVKIRPTCGA-G7-A8LD-01ALRBAchr4

151199005

-CHCHD3chr7

132481338

-
* 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
Frame-shiftENST00000535741ENST00000262570LRBAchr4

151199005

-CHCHD3chr7

132481338

-
Frame-shiftENST00000535741ENST00000448878LRBAchr4

151199005

-CHCHD3chr7

132481338

-
5CDS-5UTRENST00000535741ENST00000476546LRBAchr4

151199005

-CHCHD3chr7

132481338

-
5CDS-intronENST00000535741ENST00000542753LRBAchr4

151199005

-CHCHD3chr7

132481338

-
Frame-shiftENST00000510413ENST00000262570LRBAchr4

151199005

-CHCHD3chr7

132481338

-
Frame-shiftENST00000510413ENST00000448878LRBAchr4

151199005

-CHCHD3chr7

132481338

-
5CDS-5UTRENST00000510413ENST00000476546LRBAchr4

151199005

-CHCHD3chr7

132481338

-
5CDS-intronENST00000510413ENST00000542753LRBAchr4

151199005

-CHCHD3chr7

132481338

-
5UTR-3CDSENST00000503716ENST00000262570LRBAchr4

151199005

-CHCHD3chr7

132481338

-
5UTR-3CDSENST00000503716ENST00000448878LRBAchr4

151199005

-CHCHD3chr7

132481338

-
5UTR-5UTRENST00000503716ENST00000476546LRBAchr4

151199005

-CHCHD3chr7

132481338

-
5UTR-intronENST00000503716ENST00000542753LRBAchr4

151199005

-CHCHD3chr7

132481338

-
Frame-shiftENST00000357115ENST00000262570LRBAchr4

151199005

-CHCHD3chr7

132481338

-
Frame-shiftENST00000357115ENST00000448878LRBAchr4

151199005

-CHCHD3chr7

132481338

-
5CDS-5UTRENST00000357115ENST00000476546LRBAchr4

151199005

-CHCHD3chr7

132481338

-
5CDS-intronENST00000357115ENST00000542753LRBAchr4

151199005

-CHCHD3chr7

132481338

-
intron-3CDSENST00000507224ENST00000262570LRBAchr4

151199005

-CHCHD3chr7

132481338

-
intron-3CDSENST00000507224ENST00000448878LRBAchr4

151199005

-CHCHD3chr7

132481338

-
intron-5UTRENST00000507224ENST00000476546LRBAchr4

151199005

-CHCHD3chr7

132481338

-
intron-intronENST00000507224ENST00000542753LRBAchr4

151199005

-CHCHD3chr7

132481338

-

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FusionProtFeatures for LRBA_CHCHD3


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

P50851

CHCHD3

Q9NX63

May be involved in coupling signal transduction andvesicle trafficking to enable polarized secretion and/or membranedeposition of immune effector molecules. {ECO:0000250}. Component of the MICOS complex, a large protein complexof the mitochondrial inner membrane that plays crucial roles inthe maintenance of crista junctions, inner membrane architecture,and formation of contact sites to the outer membrane. Has alsobeen shown to function as a transcription factor which binds tothe BAG1 promoter and represses BAG1 transcription. Plays animportant role in the maintenance of the MICOS complex stabilityand the mitochondrial cristae morphology (PubMed:25781180).{ECO:0000269|PubMed:22567091, ECO:0000269|PubMed:25781180}.

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 LRBA_CHCHD3


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 LRBA_CHCHD3


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
LRBATUSC2, NOTCH1, FN1, BAG3, CAST, KIF15, DCAF11, INPPL1, MLF2, VCP, MOV10, RIC3, CT55, PARP16, RD3, TMEM52B, MED4, TMEM17, TMEM216, NCR3LG1, PVR, FAM196A, EPHA1, GYPB, DLK2, TRIM25CHCHD3KRTAP4-12, CCDC85B, UBC, MINOS1, NUDT3, TCF3, SNRPD3, ECT2, MDC1, FMNL1, MYC, PAN2, NPM1, HDAC8, PARK2, GPRASP2, GOLGA2, TRIM27, TRAF1, BLZF1, PDE4DIP, CALCOCO2, SPAG5, SAMM50, FANCL, RPGRIP1, GMCL1P1, CCDC33, USHBP1, LZTS2, RAB3IP, SSX2IP, KRT40, SPERT, NOTCH2NL, CUL7, OBSL1, CCDC8, EZH2, SUZ12, RNF2, EGFR, NTRK1, NDUFA8, AMOTL2, MYO1C, RAB2A, RAB5C, RAB7A, VAPA, TOMM40, MTX2, TRIM29, TOR1AIP1, GOLT1B, DNAJC11, MYO19, MMGT1, C19orf70, APOOL, OCIAD1, NDUFA4, ADCK1, C15orf48, DUSP22, RAB8A, NCL, COQ2, DLST, PDHA1, SDHA, VDAC1, TRIM25, G3BP1


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 LRBA_CHCHD3


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 LRBA_CHCHD3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneLRBAC3553512IMMUNODEFICIENCY, COMMON VARIABLE, 8, WITH AUTOIMMUNITY1ORPHANET;UNIPROT
TgeneCHCHD3C0236969Substance-Related Disorders1CTD_human