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	Fusion Gene Summary
	Fusion Gene Breakpoints
	Tumorigenic MoA (Mechanism of Action) Scenarios of Fusion Geness
	Fusion Genomic Features
	Fusion Gene ORF Annotations
	Fusion Protein Retained/Non-Retained Functional Features
	Fusion Transcript Sequences
	Fusion Protein Sequences
	Personalized Fusion Protein Sequences
	Fusion Gene Expressed Samples
	Related Drugs

Fusion gene:AMBRA1_HARBI1 (FusionGDB2 ID:HG55626TG283254)

Fusion Gene Summary for AMBRA1_HARBI1

Fusion gene summary

Fusion gene information	Fusion gene name: AMBRA1_HARBI1
	Fusion gene ID: hg55626tg283254
		Hgene	Tgene
	Gene symbol	AMBRA1	HARBI1
	Gene ID	55626	283254
	Gene name	autophagy and beclin 1 regulator 1	harbinger transposase derived 1
	Synonyms	DCAF3|WDR94	C11orf77
	Cytomap	11p11.2	11p11.2
	Type of gene	protein-coding	protein-coding
	Description	activating molecule in BECN1-regulated autophagy protein 1DDB1 and CUL4 associated factor 3WD repeat domain 94activating molecule in beclin-1-regulated autophagyautophagy/beclin-1 regulator 1	putative nuclease HARBI1harbinger transposase-derived nuclease
	Modification date	20240411	20240305
	UniProtAcc	.	.
	Ensembl transtripts involved in fusion gene	ENST00000528950, ENST00000533727,  ENST00000534300, ENST00000298834,  ENST00000314845, ENST00000426438,  ENST00000458649, ENST00000529963,
Fusion gene scores	* DoF score	* DoF score (Degree of Frequency) = # partners X # break points X # disease types 23 X 20 X 25=11500	* DoF score (Degree of Frequency) = # partners X # break points X # disease types 3 X 3 X 10=90
	# samples	91	14
	** MAII score	** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10) log2(91/11500*10)=-3.65962350563304 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10) log2(14/90*10)=0.637429920615292 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0
Context	PubMed: AMBRA1 [Title/Abstract] AND HARBI1 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint	AMBRA1(46615377)-HARBI1(46625459), # samples:5

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Fusion Gene Breakpoints for AMBRA1_HARBI1

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.

DNA-seq based exon junction arranged fusion gene breakpoints from dbVar. For the expressed sample information, go to Fusion Gene Sample section.

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Tumorigenic MoA (Mechanism of Action) Scenarios of Fusion Genes for AMBRA1_HARBI1

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 Fusions	Aberrant Chimeric Transcription Factor / Fusion Transcription Factor Activity	Epigenetic Reprogramming / Histone Modifier Dysregulation	Chromatin Remodeling Dysregulation	Condensate-Driven Transcriptional Rewiring / LLP	Promoter / Enhancer Hijacking	Dominant-Negative Antagonism	Cell Cycle / Checkpoint Bypass / RNA Processing Dysregulation	Subcellular Mislocalization / Spatial Dysregulation	Nuclear Body / Sub-organellar Architecture Disruption & Differentiation Blockade

* Strict version: Restricted to high- or medium-confidence fusion-specific evidence.

Fusion Gene Name

Mechanism Category

Mechanism PubMed

Tumorigenic Scenarios

Tumorigenic Scenario PubMed

Targeting Points

Targeting PubMed

Mechanism Background

Mechanism Background PubMed

* Extended version: Includes all strict-level fusion evidence plus broader gene-, pathway-, and low-confidence contextual evidence.

Fusion Gene Name

Mechanism Category

Mechanism PubMed

Tumorigenic Scenarios

Tumorigenic Scenario PubMed

Targeting Points

Targeting PubMed

Mechanism Background

Mechanism Background PubMed

Main function of each fusion partner protein. (from UniProt)

Hgene	Tgene
.	.

Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner	Gene	GO ID	GO term	PubMed ID
Hgene	AMBRA1	GO:0000045	autophagosome assembly	20921139
Hgene	AMBRA1	GO:0000209	protein polyubiquitination	30217973
Hgene	AMBRA1	GO:0000423	mitophagy	21753002
Hgene	AMBRA1	GO:0010508	positive regulation of autophagy	21358617|31123703
Hgene	AMBRA1	GO:0035307	positive regulation of protein dephosphorylation	25438055|30513302
Hgene	AMBRA1	GO:0043161	proteasome-mediated ubiquitin-dependent protein catabolic process	33854232|33854235|33854239
Hgene	AMBRA1	GO:0045591	positive regulation of regulatory T cell differentiation	30513302
Hgene	AMBRA1	GO:0051897	positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction	21753002
Hgene	AMBRA1	GO:0098780	response to mitochondrial depolarisation	21753002
Hgene	AMBRA1	GO:1901526	positive regulation of mitophagy	30217973
Hgene	AMBRA1	GO:1904544	positive regulation of free ubiquitin chain polymerization	31123703
Hgene	AMBRA1	GO:2000045	regulation of G1/S transition of mitotic cell cycle	25438055

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Fusion Genomic Features for AMBRA1_HARBI1

FusionAI 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.

Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	1-p	p (fusion gene breakpoint)
AMBRA1	chr11	46563494	-	HARBI1	chr11	46625459	-	6.30e-03	9.94e-01
AMBRA1	chr11	46615377	-	HARBI1	chr11	46625459	-	8.55e-07	1.00e+00
AMBRA1	chr11	46615377	-	HARBI1	chr11	46637931	-	1.32e-01	8.68e-01

FusionAI 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).

Hgene

Hchr

Hbp

Hstrand

Tgene

Tchr

Tbp

Tstrand

1-p

p (fusion gene breakpoint)

FusionAI 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).

Hgene

Hchr

Hbp

Hstrand

Tgene

Tchr

Tbp

Tstrand

1-p

p (fusion gene breakpoint)

Distribution 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 AMBRA1_HARBI1

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.

ORFfinder Result Based On The Fusion Transcript Sequences of the In-frame Fusion Genes.

ORFfinder Result Based On The Fusion Transcript Sequences of the 5UTR-3CDS Fusion Genes for N-Truncated Protein Search.

ORFfinder Result Based On The Fusion Transcript Sequences of the 5CDS-3UTR Fusion Genes for C-Truncated Protein Search.

DeepORF 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.

DeepORF Prediction of The Coding Potential Based on The Fusion Transcript Sequence of 5UTR-3CDS Fusion Genes (Potential N-Truncated Proteins).

DeepORF Prediction of The Coding Potential Based on The Fusion Transcript Sequence of 5CDS-3UTR Fusion Genes (Potential C-Truncated Proteins).

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Fusion Protein Retained/Non-Retained Functional Features for AMBRA1_HARBI1

Protein 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.

- In-frame and retained protein feature among the 13 regional features (visualization across fusion protein length).

- In-frame and not-retained protein feature among the 13 regional features.

- Retained PPIs in in-frame fusion.

Partner

Hgene

Hbp

Tgene

Tbp

ENST

UniProt

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Still interaction with

- Lost PPIs in in-frame fusion.

Partner

Hgene

Hbp

Tgene

Tbp

ENST

UniProt

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

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Fusion Transcript Sequence for AMBRA1_HARBI1

In-frame Fusion Transcript Sequences.

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

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

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Fusion Protein Sequence for AMBRA1_HARBI1

In-frame Fusion Protein Sequences.

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

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

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Personalized Fusion Protein Sequence for AMBRA1_HARBI1

TCGA Kinase/DNA-binding Domain Mutated Fusion Protein Sequences

CCLE Kinase/DNA-binding Domain Mutated Fusion Protein Sequences

TCGA All Mutated Fusion Protein Sequences

CCLE All Mutated Fusion Protein Sequences

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Fusion Gene Exprssed Samples for AMBRA1_HARBI1

RNA-seq based fusion gene expressed samples.

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Related Drugs for AMBRA1_HARBI1

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.

Drugs targeting genes involved in this fusion gene. (DrugBank Version 5.1.8 2021-05-08)