Fusion Gene Studies
in Kim Lab

FusionBase FusionGDB FusionGDB2 FusionPDB FusionNeoAntigen FusionAI FusionNW FGviewer Publication Contact
FusionGDB Logo

Home

Download

Statistics

Examples

Help

Contact

Center for Computational Systems Medicine
leaf

Fusion Gene Summary

leaf

Fusion Gene ORF analysis

leaf

Fusion Genomic Features

leaf

Fusion Protein Features

leaf

Fusion Gene Sequence

leaf

Fusion Gene PPI analysis

leaf

Related Drugs

leaf

Related Diseases

Fusion gene:AFG3L2-IGKC (FusionGDB2 ID:HG10939TG3514)

Fusion Gene Summary for AFG3L2-IGKC

check button Fusion gene summary
Fusion gene informationFusion gene name: AFG3L2-IGKC
Fusion gene ID: hg10939tg3514
HgeneTgene
Gene symbol

AFG3L2

IGKC

Gene ID

10939

3514

Gene nameAFG3 like matrix AAA peptidase subunit 2
SynonymsSCA28|SPAX5
Cytomap('AFG3L2')('IGKC')

18p11.21

Type of geneprotein-coding
DescriptionAFG3-like protein 2AFG3 ATPase family gene 3-like 2AFG3 ATPase family member 3-like 2AFG3 like AAA ATPase 2ATPase family gene 3, yeastparaplegin-like protein
Modification date20200313
UniProtAcc

Q9Y4W6

P01834

Ensembl transtripts involved in fusion geneENST00000269143, 
Fusion gene scores* DoF score7 X 8 X 6=336160 X 66 X 20=211200
# samples 8149
** MAII scorelog2(8/336*10)=-2.0703893278914
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(149/211200*10)=-7.14715369378365
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: AFG3L2 [Title/Abstract] AND IGKC [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointAFG3L2(12358733)-IGKC(89157198), # samples:1
AFG3L2(12358734)-IGKC(89157199), # 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
HgeneAFG3L2

GO:0033619

membrane protein proteolysis

22354088



check button Fusion gene information
* 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
ChimerDB4HNSCTCGA-CR-7391AFG3L2chr18

12358733

-IGKCchr2

89157198

-
ChimerDB4LUSCTCGA-18-3406AFG3L2chr18

12358734

-IGKCchr2

89157199

-


Top

Fusion Gene ORF analysis for AFG3L2-IGKC

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-3CDSENST00000269143ENST00000390237AFG3L2chr18

12358733

-IGKCchr2

89157198

-
intron-3CDSENST00000269143ENST00000390237AFG3L2chr18

12358734

-IGKCchr2

89157199

-

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

Top

Fusion Genomic Features for AFG3L2-IGKC


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)


Top

Fusion Protein Features for AFG3L2-IGKC


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/:12358733/:89157198)
- 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
AFG3L2

Q9Y4W6

IGKC

P01834

FUNCTION: ATP-dependent protease which is essential for axonal and neuron development. In neurons, mediates degradation of SMDT1/EMRE before its assembly with the uniporter complex, limiting the availability of SMDT1/EMRE for MCU assembly and promoting efficient assembly of gatekeeper subunits with MCU (PubMed:27642048). Required for the maturation of paraplegin (SPG7) after its cleavage by mitochondrial-processing peptidase (MPP), converting it into a proteolytically active mature form (By similarity). Required for the maturation of PINK1 into its 52kDa mature form after its cleavage by mitochondrial-processing peptidase (MPP) (PubMed:22354088). {ECO:0000250|UniProtKB:Q8JZQ2, ECO:0000269|PubMed:22354088, ECO:0000269|PubMed:27642048}.FUNCTION: Constant region of immunoglobulin light chains. Immunoglobulins, also known as antibodies, are membrane-bound or secreted glycoproteins produced by B lymphocytes. In the recognition phase of humoral immunity, the membrane-bound immunoglobulins serve as receptors which, upon binding of a specific antigen, trigger the clonal expansion and differentiation of B lymphocytes into immunoglobulins-secreting plasma cells. Secreted immunoglobulins mediate the effector phase of humoral immunity, which results in the elimination of bound antigens (PubMed:22158414, PubMed:20176268). The antigen binding site is formed by the variable domain of one heavy chain, together with that of its associated light chain. Thus, each immunoglobulin has two antigen binding sites with remarkable affinity for a particular antigen. The variable domains are assembled by a process called V-(D)-J rearrangement and can then be subjected to somatic hypermutations which, after exposure to antigen and selection, allow affinity maturation for a particular antigen (PubMed:17576170, PubMed:20176268). {ECO:0000303|PubMed:17576170, ECO:0000303|PubMed:20176268, ECO:0000303|PubMed:22158414}.

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


Top

Fusion Gene Sequence for AFG3L2-IGKC


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.

Top

Fusion Gene PPI Analysis for AFG3L2-IGKC


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


Top

Related Drugs for AFG3L2-IGKC


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

Top

Related Diseases for AFG3L2-IGKC


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneAFG3L2C1853249SPINOCEREBELLAR ATAXIA 2810CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneAFG3L2C3280977SPASTIC ATAXIA 5, AUTOSOMAL RECESSIVE5CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneAFG3L2C0087012Ataxia, Spinocerebellar1CTD_human
HgeneAFG3L2C0751776Atypical Inclusion-Body Disease1CTD_human
HgeneAFG3L2C0751777Familial Progressive Myoclonic Epilepsy1CTD_human
HgeneAFG3L2C0751778Myoclonic Epilepsies, Progressive1CTD_human
HgeneAFG3L2C0751779Action Myoclonus-Renal Failure Syndrome1CTD_human
HgeneAFG3L2C0751780Biotin-Responsive Encephalopathy1CTD_human
HgeneAFG3L2C0751781Dentatorubral-Pallidoluysian Atrophy1CTD_human
HgeneAFG3L2C0751782May-White Syndrome1CTD_human
HgeneAFG3L2C0752120Spinocerebellar Ataxia Type 11CTD_human
HgeneAFG3L2C0752121Spinocerebellar Ataxia Type 21CTD_human
HgeneAFG3L2C0752122Spinocerebellar Ataxia Type 41CTD_human
HgeneAFG3L2C0752123Spinocerebellar Ataxia Type 51CTD_human
HgeneAFG3L2C0752124Spinocerebellar Ataxia Type 6 (disorder)1CTD_human
HgeneAFG3L2C0752125Spinocerebellar Ataxia Type 71CTD_human
TgeneC3279824Kappa-Chain Deficiency2CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC0013374Dysgammaglobulinemia1CTD_human
TgeneC0019209Hepatomegaly1CTD_human
TgeneC0027121Myositis1CTD_human
TgeneC0158353Infectious Myositis1CTD_human
TgeneC0231221Asymptomatic1GENOMICS_ENGLAND
TgeneC0544796Myositis, Proliferative1CTD_human
TgeneC0751356Idiopathic Inflammatory Myopathies1CTD_human
TgeneC0751357Myositis, Focal1CTD_human