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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene Breakpoints

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Tumorigenic MoA (Mechanism of Action) Scenarios of Fusion Geness

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Fusion Genomic Features

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Fusion Gene ORF Annotations

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Fusion Protein Retained/Non-Retained Functional Features

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Fusion Transcript Sequences

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Fusion Protein Sequences

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Personalized Fusion Protein Sequences

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Fusion Gene Expressed Samples

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Related Drugs

Fusion gene:YIPF4_BIRC6 (FusionGDB2 ID:HG84272TG57448)

Fusion Gene Summary for YIPF4_BIRC6

check button Fusion gene summary
Fusion gene informationFusion gene name: YIPF4_BIRC6
Fusion gene ID: hg84272tg57448
HgeneTgene
Gene symbol

YIPF4

BIRC6

Gene ID

84272

57448

Gene nameYip1 domain family member 4baculoviral IAP repeat containing 6
SynonymsFinGER4|Nbla11189|YIPFalpha2APOLLON|BRUCE
Cytomap

2p22.3

2p22.3

Type of geneprotein-codingprotein-coding
Descriptionprotein YIPF4YIP1 family member 4putative protein product of Nbla11189baculoviral IAP repeat-containing protein 6BIR repeat-containing ubiquitin-conjugating enzymeRING-type E3 ubiquitin transferase BIRC6ubiquitin-conjugating BIR-domain enzyme apollon
Modification date2024040720240407
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000238831, 
Fusion gene scores* DoF score* DoF score (Degree of Frequency) = # partners X # break points X # disease types
6 X 6 X 6=216		* DoF score (Degree of Frequency) = # partners X # break points X # disease types
10 X 28 X 21=5880
# samples 2863
** MAII score** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)
log2(28/216*10)=0.374395514781498
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0		** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)
log2(63/5880*10)=-3.22239242133645
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: YIPF4 [Title/Abstract] AND BIRC6 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint

check buttonFusion gene breakpoints across YIPF4 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure
check buttonFusion gene breakpoints across BIRC6 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

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Fusion Gene Breakpoints for YIPF4_BIRC6


check button RNA-seq based exon junction arranged fusion gene breakpoints from 8 resources (TCGA, CCLE, cBioPortal, GenBank, ChimerDB, ChimerKB, ChildHoodFusions, and GTEx). For the expressed sample information, go to Fusion Gene Sample section.
HgeneHchrHbpTgeneTchrTbp
YIPF4chr232532259BIRC6chr232602656
YIPF4chr232503303BIRC6chr232503303


check button DNA-seq based exon junction arranged fusion gene breakpoints from dbVar. For the expressed sample information, go to Fusion Gene Sample section.
HgeneHchrHbpTgeneTchrTbpSV type
YIPF4chr232514528BIRC6chr232806011DUP
YIPF4chr232526448BIRC6chr232668659DUP
YIPF4chr232513516BIRC6chr232614845DUP
YIPF4chr232509330BIRC6chr232808804DEL
YIPF4chr232531681BIRC6chr232667562DEL
YIPF4chr232531681BIRC6chr232808804DEL
YIPF4chr232531681BIRC6chr232633569DEL
YIPF4chr232531681BIRC6chr232822957DEL
YIPF4chr232531681BIRC6chr232691438DEL
YIPF4chr232531681BIRC6chr232679732DEL
YIPF4chr232531681BIRC6chr232735881DEL
YIPF4chr232537255BIRC6chr232775984DEL


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Tumorigenic MoA (Mechanism of Action) Scenarios of Fusion Genes for YIPF4_BIRC6


check button To generate these tumorigenic scenario annotations, we implemented a deduction-first, retrieval-later computational framework. The pipeline first applies rule-guided reasoning across ten core mechanistic categories (M1–M10) derived from fusion gene biology to infer candidate mechanisms, tumorigenic scenarios, targeting points, and targeting backgrounds. To ensure empirical accountability, a governed Python workflow retrieves literature candidates via NCBI E-utilities and Europe PMC using tiered searches. Using JSON Schema-constrained LLM evidence judges (GPT-5.6 Luna and Terra), retrieved articles are evaluated for specificity and confidence without de novo PMID generation. This produces two distinct versions: a strict version restricted to high- or medium-confidence fusion-specific evidence, and an extended version incorporating broader gene-, pathway-, and contextual evidence.
* We have 10 tumorigenic mechanism categories of fusion genes as shown below.
Constitutively Active Kinases, Catalytic Domain Dysregulation, & Transmembrane Ligand FusionsAberrant Chimeric Transcription Factor / Fusion Transcription Factor ActivityEpigenetic Reprogramming / Histone Modifier DysregulationChromatin Remodeling DysregulationCondensate-Driven Transcriptional Rewiring / LLPPromoter / Enhancer HijackingDominant-Negative AntagonismCell Cycle / Checkpoint Bypass / RNA Processing DysregulationSubcellular Mislocalization / Spatial DysregulationNuclear Body / Sub-organellar Architecture Disruption & Differentiation Blockade

* Strict version: Restricted to high- or medium-confidence fusion-specific evidence.
Fusion Gene NameMechanism CategoryMechanism PubMedTumorigenic ScenariosTumorigenic Scenario PubMedTargeting PointsTargeting PubMedMechanism BackgroundMechanism Background PubMed

* Extended version: Includes all strict-level fusion evidence plus broader gene-, pathway-, and low-confidence contextual evidence.
Fusion Gene NameMechanism CategoryMechanism PubMedTumorigenic ScenariosTumorigenic Scenario PubMedTargeting PointsTargeting PubMedMechanism BackgroundMechanism Background PubMed

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

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

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Fusion Genomic Features for YIPF4_BIRC6


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) of In-frame fusion genes. 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 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) of 5UTR-3CSD fusion genes (N-truncated cases).
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)

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) of 5CDS-3UTR fusion genes (C-truncated cases).
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)

check buttonDistribution of six genomic regulatory feature tracks across a ±5 kb window centered on the fusion breakpoints. We input the breakpoint sequences into AlphaGenome and obtained predicted genome tracks at single-base-pair resolution for each modality by running a single forward pass over the reference sequence. Specifically, for each breakpoint, AlphaGenome processed and returned predicted track data across diverse modalities, which were then averaged across all tracks within each output type and visualized across the ±5 kb window. The left panel shows the 5'-gene breakpoint ±5 kb area, and the right panel shows the 3'-gene breakpoint area, with tracks grouped by category: chromatin accessibility (DNase-seq, ATAC-seq), active transcription (RNA-seq, CAGE), and chromatin binding (ChIP-Histone, ChIP-TF).

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Fusion Gene ORF Annotations for YIPF4_BIRC6

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

check buttonORFfinder Result Based On The Fusion Transcript Sequences of the In-frame Fusion Genes.
HenstTenstHgeneHchrHbpTgeneTchrTbpSeq length
(transcript)		Seq length
(peptide)

check buttonORFfinder Result Based On The Fusion Transcript Sequences of the 5UTR-3CDS Fusion Genes for N-Truncated Protein Search.
HenstTenstHgeneHchrHbpTgeneTchrTbpSeq length
(transcript)		Seq length
(peptide)

check buttonORFfinder Result Based On The Fusion Transcript Sequences of the 5CDS-3UTR Fusion Genes for C-Truncated Protein Search.
HenstTenstHgeneHchrHbpTgeneTchrTbpSeq length
(transcript)		Seq length
(peptide)

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.
HenstTenstHgeneHchrHbpTgeneTchrTbpNo-coding scoreCoding score

check buttonDeepORF Prediction of The Coding Potential Based on The Fusion Transcript Sequence of 5UTR-3CDS Fusion Genes (Potential N-Truncated Proteins).
HenstTenstHgeneHchrHbpTgeneTchrTbpNo-coding scoreCoding score

check buttonDeepORF Prediction of The Coding Potential Based on The Fusion Transcript Sequence of 5CDS-3UTR Fusion Genes (Potential C-Truncated Proteins).
HenstTenstHgeneHchrHbpTgeneTchrTbpNo-coding scoreCoding score

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Fusion Protein Retained/Non-Retained Functional Features for YIPF4_BIRC6

check buttonProtein Level Annotation from FGviewer
* Retention 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.
fgviewer annotation
- In-frame and retained protein feature among the 13 regional features (visualization across fusion protein length).
No matching images found for ${hg}_${tg}.

- In-frame and retained protein feature among the 13 regional features (texts).
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


check button - Retained PPIs in in-frame fusion.
PartnerHgeneHbpTgeneTbpENSTUniProtStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerHgeneHbpTgeneTbpENSTUniProtStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Fusion Transcript Sequence for YIPF4_BIRC6

check button In-frame Fusion Transcript Sequences.

check button N-Truncated Transcript (5UTR-3CDS) Sequences

check button C-Truncated Transcript (5CDS-3UTR) Sequences

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Fusion Protein Sequence for YIPF4_BIRC6

check button In-frame Fusion Protein Sequences.

check button N-Truncated Protein (5UTR-3CDS) Sequences

check button C-Truncated Protein (5CDS-3UTR) Sequences

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Personalized Fusion Protein Sequence for YIPF4_BIRC6


check button TCGA Kinase/DNA-binding Domain Mutated Fusion Protein Sequences
NumGene GroupDomain LociFusion Protein IDFusion Gene NamePartnerMutated Residue in WT ProteinSeq. LengthMutated Residue in Fusion Protein

check button CCLE Kinase/DNA-binding Domain Mutated Fusion Protein Sequences

NumGene GroupDomain LociFusion Protein IDFusion Gene NamePartnerMutated Residue in WT ProteinSeq. LengthMutated Residue in Fusion Protein

check button TCGA All Mutated Fusion Protein Sequences


Fusion Protein IDSample IDMutated PartnerAAchange in WTSeq. LengthAAchange in Fusion

check button CCLE All Mutated Fusion Protein Sequences


Fusion Protein IDSample IDMutated PartnerAAchange in WTSeq. LengthAAchange in Fusion

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Fusion Gene Exprssed Samples for YIPF4_BIRC6


check buttonRNA-seq based fusion gene expressed samples.
SourceStudyDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
GTExtissueSRR1097270YIPF4

chr2

32532259+BIRC6

chr2

32602656

+
GTExtissueSRR1102418YIPF4

chr2

32532259+BIRC6

chr2

32602656

+
GTExtissueSRR1334939YIPF4

chr2

32532259+BIRC6

chr2

32602656

+
GTExtissueSRR1353686YIPF4

chr2

32532259+BIRC6

chr2

32602656

+
GTExtissueSRR1362438YIPF4

chr2

32532259+BIRC6

chr2

32602656

+
GTExtissueSRR1368240YIPF4

chr2

32532259+BIRC6

chr2

32602656

+
GTExtissueSRR1386945YIPF4

chr2

32532259+BIRC6

chr2

32602656

+
GTExtissueSRR1390160YIPF4

chr2

32532259+BIRC6

chr2

32602656

+
GTExtissueSRR1454995YIPF4

chr2

32532259+BIRC6

chr2

32602656

+
GTExtissueSRR1455038YIPF4

chr2

32532259+BIRC6

chr2

32602656

+
GTExtissueSRR1455236YIPF4

chr2

32532259+BIRC6

chr2

32602656

+
GTExtissueSRR1465983YIPF4

chr2

32532259+BIRC6

chr2

32602656

+
GTExtissueSRR1480384YIPF4

chr2

32532259+BIRC6

chr2

32602656

+
GTExtissueSRR613843YIPF4

chr2

32532259+BIRC6

chr2

32602656

+
GTExtissueSRR659331YIPF4

chr2

32532259+BIRC6

chr2

32602656

+
GTExtissueSRR660534YIPF4

chr2

32532259+BIRC6

chr2

32602656

+
GTExtissueSRR663783YIPF4

chr2

32532259+BIRC6

chr2

32602656

+
GTExtissueSRR811653YIPF4

chr2

32532259+BIRC6

chr2

32602656

+
GTExtissueSRR818850YIPF4

chr2

32532259+BIRC6

chr2

32602656

+
GTExtissueSRR819820YIPF4

chr2

32532259+BIRC6

chr2

32602656

+
ChimerDBSTADTCGA-EQ-8122-01AYIPF4

chr2

32503303+BIRC6

chr2

32503303

+

check buttonDNA-seq based fusion gene expressed samples.
SourceStudyDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrandSV type
dbVarnstd102Unknown_CellYIPF4

chr2

32514528BIRC6

chr2

32806011

DUP
dbVarnstd151Unknown_CellYIPF4

chr2

32526448BIRC6

chr2

32668659

DUP
dbVarnstd200Unknown_CellYIPF4

chr2

32513516BIRC6

chr2

32614845

DUP
dbVarnstd204Unknown_CellYIPF4

chr2

32513516BIRC6

chr2

32614845

DUP
dbVarnstd239Unknown_CellWG1004325-DNAB10-016925-0095480196YIPF4

chr2

32509330BIRC6

chr2

32808804

DEL
dbVarnstd239Unknown_CellWG1004329-DNAH01-015401-0095504316YIPF4

chr2

32531681BIRC6

chr2

32667562

DEL
dbVarnstd239Unknown_CellWG1004328-DNAD02-010842-0095504330YIPF4

chr2

32531681BIRC6

chr2

32808804

DEL
dbVarnstd239Unknown_CellWG1004329-DNAC12-010157-0095481588YIPF4

chr2

32531681BIRC6

chr2

32808804

DEL
dbVarnstd239Unknown_CellWG1004356-DNAE01-015049-0095504538YIPF4

chr2

32531681BIRC6

chr2

32633569

DEL
dbVarnstd239Unknown_CellWG1004360-DNAD02-016286-0095448157YIPF4

chr2

32531681BIRC6

chr2

32667562

DEL
dbVarnstd239Unknown_CellWG1004366-DNAF05-011408-0095503639YIPF4

chr2

32531681BIRC6

chr2

32822957

DEL
dbVarnstd239Unknown_CellWG1006253-DNAC01-021644-1047563673YIPF4

chr2

32531681BIRC6

chr2

32808804

DEL
dbVarnstd239Unknown_CellWG1006253-DNAC01-021644-1047563673YIPF4

chr2

32531681BIRC6

chr2

32808804

DEL
dbVarnstd239Unknown_CellWG1006260-DNAA01-023119-1047872786YIPF4

chr2

32531681BIRC6

chr2

32808804

DEL
dbVarnstd239Unknown_CellWG1006264-DNAD02-020714-1047872816YIPF4

chr2

32531681BIRC6

chr2

32822957

DEL
dbVarnstd239Unknown_CellWG1006264-DNAD02-020714-1047872816YIPF4

chr2

32531681BIRC6

chr2

32822957

DEL
dbVarnstd239Unknown_CellWG1006273-DNAB04-022443-1047872847YIPF4

chr2

32531681BIRC6

chr2

32822957

DEL
dbVarnstd239Unknown_CellWG1006280-DNAA03-023556-1047873549YIPF4

chr2

32531681BIRC6

chr2

32667562

DEL
dbVarnstd239Unknown_CellWG1006286-DNAC01-025907-1047873611YIPF4

chr2

32531681BIRC6

chr2

32691438

DEL
dbVarnstd239Unknown_CellWG1006286-DNAD01-024949-1047873616YIPF4

chr2

32531681BIRC6

chr2

32679732

DEL
dbVarnstd239Unknown_CellWG1006286-DNAD01-024949-1047873616YIPF4

chr2

32531681BIRC6

chr2

32679732

DEL
dbVarnstd239Unknown_Cell200158280160_R04C02YIPF4

chr2

32531681BIRC6

chr2

32735881

DEL
dbVarnstd239Unknown_Cell200162460053_R12C01YIPF4

chr2

32531681BIRC6

chr2

32633569

DEL
dbVarnstd239Unknown_Cell200162510057_R10C02YIPF4

chr2

32531681BIRC6

chr2

32808804

DEL
dbVarnstd239Unknown_Cell200162510157_R08C02YIPF4

chr2

32531681BIRC6

chr2

32667562

DEL
dbVarnstd239Unknown_CellWG1004320-DNAC03-012823-0095477331YIPF4

chr2

32531681BIRC6

chr2

32808804

DEL
dbVarnstd239Unknown_Cell200162510064_R10C01YIPF4

chr2

32537255BIRC6

chr2

32775984

DEL


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Related Drugs for YIPF4_BIRC6


check button PubMed Abstract Search With ['A-B' AND 'drug'], ['A::B' AND 'drug']
* For more details on the Studied, Reported, Approved Drugs targeting this fusion gene, Go to FusionPub.
PMIDFusion Gene NameDrugStudy Title

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