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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:ITM2C_FOXP1 (FusionGDB2 ID:HG81618TG27086)

Fusion Gene Summary for ITM2C_FOXP1

Fusion gene summary

Fusion gene information	Fusion gene name: ITM2C_FOXP1
	Fusion gene ID: hg81618tg27086
		Hgene	Tgene
	Gene symbol	ITM2C	FOXP1
	Gene ID	81618	27086
	Gene name	integral membrane protein 2C	forkhead box P1
	Synonyms	BRI3|BRICD2C|E25|E25C|ITM3	12CC4|HSPC215|MFH|QRF1|hFKH1B
	Cytomap	2q37.1	3p13
	Type of gene	protein-coding	protein-coding
	Description	integral membrane protein 2CBRICHOS domain containing 2Ccerebral protein 14integral membrane protein 3transmembrane protein BRI3	forkhead box protein P1fork head-related protein like Bglutamine-rich factor 1mac-1-regulated forkhead
	Modification date	20240305	20240411
	UniProtAcc	.	.
	Ensembl transtripts involved in fusion gene
Fusion gene scores	* DoF score	* DoF score (Degree of Frequency) = # partners X # break points X # disease types 8 X 6 X 10=480	* DoF score (Degree of Frequency) = # partners X # break points X # disease types 15 X 81 X 38=46170
	# samples	11	491
	** MAII score	** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10) log2(11/480*10)=-2.12553088208386 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(491/46170*10)=-3.23316080273467 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context	PubMed: ITM2C [Title/Abstract] AND FOXP1 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint

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Fusion Gene Breakpoints for ITM2C_FOXP1

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 ITM2C_FOXP1

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	ITM2C	GO:0010977	negative regulation of neuron projection development	18452648
Hgene	ITM2C	GO:0030182	neuron differentiation	18452648
Tgene	FOXP1	GO:0002903	negative regulation of B cell apoptotic process	25267198
Tgene	FOXP1	GO:0010629	negative regulation of gene expression	30111844
Tgene	FOXP1	GO:0030316	osteoclast differentiation	18799727
Tgene	FOXP1	GO:0032496	response to lipopolysaccharide	18799727
Tgene	FOXP1	GO:0032651	regulation of interleukin-1 beta production	18799727
Tgene	FOXP1	GO:0032655	regulation of interleukin-12 production	18799727
Tgene	FOXP1	GO:0032680	regulation of tumor necrosis factor production	18799727
Tgene	FOXP1	GO:0036035	osteoclast development	18799727
Tgene	FOXP1	GO:0042116	macrophage activation	18799727
Tgene	FOXP1	GO:0042117	monocyte activation	18799727
Tgene	FOXP1	GO:0045655	regulation of monocyte differentiation	15286807
Tgene	FOXP1	GO:0045892	negative regulation of DNA-templated transcription	20950788
Tgene	FOXP1	GO:0050727	regulation of inflammatory response	18799727
Tgene	FOXP1	GO:0060766	negative regulation of androgen receptor signaling pathway	18640093
Tgene	FOXP1	GO:1900424	regulation of defense response to bacterium	18799727
Tgene	FOXP1	GO:1901256	regulation of macrophage colony-stimulating factor production	18799727
Tgene	FOXP1	GO:2000341	regulation of chemokine (C-X-C motif) ligand 2 production	18799727

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Fusion Genomic Features for ITM2C_FOXP1

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)

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 ITM2C_FOXP1

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 ITM2C_FOXP1

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 ITM2C_FOXP1

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 ITM2C_FOXP1

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 ITM2C_FOXP1

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 ITM2C_FOXP1

RNA-seq based fusion gene expressed samples.

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Related Drugs for ITM2C_FOXP1

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)