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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:CMTR1_ZFAND3 (FusionGDB2 ID:HG23070TG60685)

Fusion Gene Summary for CMTR1_ZFAND3

Fusion gene summary

Fusion gene information	Fusion gene name: CMTR1_ZFAND3
	Fusion gene ID: hg23070tg60685
		Hgene	Tgene
	Gene symbol	CMTR1	ZFAND3
	Gene ID	23070	60685
	Gene name	cap methyltransferase 1	zinc finger AN1-type containing 3
	Synonyms	FTSJD2\|KIAA0082\|MTr1\|hMTr1	TEX27
	Cytomap	6p21.2	6p21.2
	Type of gene	protein-coding	protein-coding
	Description	cap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1FtsJ methyltransferase domain containing 2ISG95S-adenosyl-L-methionine-dependent methyltransferase FTSJD2cap1 2'O-ribose methyltransferase 1ftsJ methyltransferase domain-containing protein 2int	AN1-type zinc finger protein 3testis expressed sequence 27testis-expressed protein 27zinc finger, AN1-type domain 3
	Modification date	20240411	20240305
	UniProtAcc	.	.
	Ensembl transtripts involved in fusion gene	ENST00000373451, ENST00000493656,	ENST00000493656, ENST00000373451,
Fusion gene scores	* DoF score	* DoF score (Degree of Frequency) = # partners X # break points X # disease types 6 X 10 X 9=540	* DoF score (Degree of Frequency) = # partners X # break points X # disease types 7 X 26 X 20=3640
	# samples	10	35
	** MAII score	** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score10) log2(10/54010)=-2.43295940727611 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score10) log2(35/364010)=-3.37851162325373 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context	PubMed: CMTR1 [Title/Abstract] AND ZFAND3 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint	CMTR1(37445415)-ZFAND3(38120010), # samples:1

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Fusion Gene Breakpoints for CMTR1_ZFAND3

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.

Hgene	Hchr	Hbp	Tgene	Tchr	Tbp
CMTR1	chr6	37445415	ZFAND3	chr6	37445415
CMTR1	chr6	37445415	ZFAND3	chr6	38120011
CMTR1	chr6	37477639	ZFAND3	chr6	38152235

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

Hgene	Hchr	Hbp	Tgene	Tchr	Tbp	SV type
CMTR1	chr6	37446182	ZFAND3	chr6	38084520	DEL

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Tumorigenic MoA (Mechanism of Action) Scenarios of Fusion Genes for CMTR1_ZFAND3

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
CMTR1-ZFAND3	Aberrant Chimeric Transcription Factor / Fusion Transcription Factor Activity M2		CMTR1 promoter drives high ZFAND3 zinc-finger expression, facilitating nuclear invasion-associated gene transcription in glioblastoma.		Transcriptional CDK9 inhibitors; BET bromodomain inhibitors		Glioblastoma multiforme and invasive cancers

* 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
CMTR1-ZFAND3	Aberrant Chimeric Transcription Factor / Fusion Transcription Factor Activity M2	Evidence level: Indirect gene evidence; Confidence: Medium; PMID: 33311477; Title: AN1-type zinc finger protein 3 (ZFAND3) is a transcriptional regulator that drives Glioblastoma invasion.	CMTR1 promoter drives high ZFAND3 zinc-finger expression, facilitating nuclear invasion-associated gene transcription in glioblastoma.	Evidence level: Indirect gene evidence; Confidence: Medium; PMID: 33311477; Title: AN1-type zinc finger protein 3 (ZFAND3) is a transcriptional regulator that drives Glioblastoma invasion.	Transcriptional CDK9 inhibitors; BET bromodomain inhibitors		Glioblastoma multiforme and invasive cancers	Evidence level: Indirect gene evidence; Confidence: Medium; PMID: 33311477; Title: AN1-type zinc finger protein 3 (ZFAND3) is a transcriptional regulator that drives Glioblastoma invasion.

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	CMTR1	GO:0006370	7-methylguanosine mRNA capping	21310715
Hgene	CMTR1	GO:0016556	mRNA modification	20713356

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Fusion Genomic Features for CMTR1_ZFAND3

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)
CMTR1	chr6	37445415	+	ZFAND3	chr6	38120010	+	2.04e-05	1.00e+00

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 CMTR1_ZFAND3

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.

ORF	Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
5CDS-3UTR	ENST00000373451	ENST00000463847	CMTR1	chr6	37445415	+	ZFAND3	chr6	38120010	+
Frame-shift	ENST00000373451	ENST00000287218	CMTR1	chr6	37445415	+	ZFAND3	chr6	38120010	+
Frame-shift	ENST00000373451	ENST00000373391	CMTR1	chr6	37445415	+	ZFAND3	chr6	38120010	+

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

Henst

Tenst

Hgene

Hchr

Hbp

Tgene

Tchr

Tbp

Seq length
(transcript)

Seq length
(peptide)

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

Henst

Tenst

Hgene

Hchr

Hbp

Tgene

Tchr

Tbp

Seq length
(transcript)

Seq length
(peptide)

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

Henst

Tenst

Hgene

Hchr

Hbp

Tgene

Tchr

Tbp

Seq length
(transcript)

Seq length
(peptide)

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.

Henst

Tenst

Hgene

Hchr

Hbp

Tgene

Tchr

Tbp

No-coding score

Coding score

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

Henst

Tenst

Hgene

Hchr

Hbp

Tgene

Tchr

Tbp

No-coding score

Coding score

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

Henst	Tenst	Hgene	Hchr	Hbp	Tgene	Tchr	Tbp	No-coding score	Coding score
ENST00000373451	ENST00000463847	CMTR1	chr6	37445415	ZFAND3	chr6	38120010	0.00e+00	3.08e-02

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Fusion Protein Retained/Non-Retained Functional Features for CMTR1_ZFAND3

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).

No matching images found for ${hg}_${tg}.

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

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

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

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

- 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 CMTR1_ZFAND3

In-frame Fusion Transcript Sequences.

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

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

>CMTR1_ZFAND3_ENST00000373451_ENST00000463847_37445415_38120010 length=2317nt 
 Breakpoint=2317nt
CGCAGTACTGGACCCGAGCGCGACGGTGCGGCTGGCGGACCCGGGCTGGCTTGTGGGGAAACGAAACTGAGGGAGGAGGCGGCGGCTCTGGCAGCGGCGGCGACAGTGTCGGCCTGACCCCCCCTCCGCTCCCCGGCAGCTCGCTCTCTC
CCCTCAGCTTAACGATGAAGAGGAGAACTGACCCAGAATGCACTGCCCCCATCAAGAAACAGAAAAAAAGAGTTGCAGAGCTTGCCCTGAGCCTCAGCTCCACGTCCGATGATGAACCTCCCTCCTCTGTCAGTCATGGAGCAAAAGCAT
CTACTACAAGCCTTAGTGGGTCTGATAGTGAGACCGAGGGGAAACAACACAGCTCTGACTCTTTTGACGATGCATTCAAAGCAGACTCTCTTGTGGAAGGAACTTCTTCTCGCTATTCCATGTATAATAGCGTCTCCCAGAAGCTTATGG
CCAAGATGGGCTTCAGGGAAGGTGAAGGATTGGGTAAATACAGCCAGGGTCGGAAGGACATCGTTGAGGCTTCCAGTCAGAAAGGTCGAAGAGGCTTGGGTCTGACACTCCGGGGCTTTGACCAGGAGCTGAACGTGGACTGGCGAGATG
AGCCAGAGCCCAGTGCTTGTGAGCAGGTGTCATGGTTTCCAGAATGTACCACTGAAATTCCTGACACTCAGGAAATGAGCGATTGGATGGTGGTGGGAAAGAGAAAGATGATTATTGAAGATGAAACAGAGTTTTGTGGGGAAGAGCTGC
TTCACAGTGTGTTGCAGTGTAAGAGCGTGTTTGATGTCTTGGATGGGGAAGAGATGCGGCGAGCTCGGACTCGGGCCAATCCCTATGAGATGATCCGAGGAGTCTTCTTTCTAAACAGGGCAGCAATGAAGATGGCTAACATGGATTTTG
TATTTGATCGCATGTTCACAAATCCGCGGGACTCTTATGGGAAGCCACTGGTGAAGGACCGGGAAGCTGAGCTTCTGTACTTTGCTGATGTCTGCGCAGGCCCAGGTGGCTTCTCAGAGTATGTGCTGTGGAGGAAGAAGTGGCATGCAA
AGGGCTTTGGAATGACTTTGAAGGGCCCTAATGACTTCAAGCTGGAGGACTTCTACTCTGCTTCCAGTGAACTCTTCGAACCCTACTATGGTGAGGGTGGGATTGATGGAGATGGAGATATCACCCGCCCAGAGAACATCTCTGCTTTTC
GGAATTTTGTCCTGGATAACACAGATCGCAAGGGTGTCCATTTTCTGATGGCTGATGGGGGTTTCTCGGTGGAGGGGCAGGAGAACCTGCAGGAGATCCTCAGCAAGCAGCTGCTTCTGTGTCAGTTCCTCATGGCGCTGTCCATTGTCC
GGACAGGAGGCCACTTCATCTGTAAAACCTTTGACCTGTTCACACCGTTTAGTGTGGGGCTTGTCTACCTGCTGTACTGCTGCTTTGAACGAGTTTGTCTCTTCAAGCCTATTACCAGCCGTCCTGCCAACTCAGAGAGGTATGTGGTGT
GCAAGGGCCTGAAGGTGGGCATAGATGATGTTCGGGATTACCTCTTCGCAGTGAATATTAAACTCAATCAGCTGCGGAACACGGATTCCGACGTCAACTTGGTGGTCCCCCTGGAGGTGATCAAGGGAGACCATGAATTTACTGACTACA
TGATACGGTCCAATGAGAGCCACTGTAGTCTGCAGATCAAAGCTCTGGCGAAAATCCATGCCTTTGTTCAAGACACGACACTGAGTGAGCCTCGACAGGCAGAGATACGGAAGGAGTGCCTCCGACTCTGGGGGATCCCAGACCAGGCTC
GTGTGGCTCCTTCTTCCTCCGACCCTAAATCGAAGTTCTTTGAGCTAATCCAGGGCACTGAGATTGACATCTTCAGCTACAAGCCCACACTGCTCACCTCTAAAACCCTGGAGAAGATCCGCCCTGTGTTTGACTACCGCTGCATGGTAT
CTGGCAGTGAGCAGAAGTTCCTCATCGGCCTGGGGAAATCCCAGATCTACACATGGGATGGCCGCCAGTCAGACCGCTGGATCAAGCTAGACCTGAAGACAGAGCTGCCCCGGGACACTCTGCTATCTGTGGAAATTGTGCATGAGCTGA
AAGGGGAGGGGAAGGCCCAGAGGAAGATCAGTGCCATCCACATCCTCGATGTCCTTGTGCTGAATGGCACCGACGTTCGGGAGCAGCACTTTAACCAGCGAATTCAGCTTGCCGAGAAATTTGTGAAAGCCGTTTCCAAGCCTAGTCGGC
CCGACATGAATCCCATCAGGGTGAAGGAGGTGTACAGACTGGAAGAGATGGAGAAGATTTTTGTCAG

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Fusion Protein Sequence for CMTR1_ZFAND3

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 CMTR1_ZFAND3

TCGA Kinase/DNA-binding Domain Mutated Fusion Protein Sequences

Num

Gene Group

Domain Loci

Fusion Protein ID

Fusion Gene Name

Partner

Mutated Residue in WT Protein

Seq. Length

Mutated Residue in Fusion Protein

CCLE Kinase/DNA-binding Domain Mutated Fusion Protein Sequences

Num

Gene Group

Domain Loci

Fusion Protein ID

Fusion Gene Name

Partner

Mutated Residue in WT Protein

Seq. Length

Mutated Residue in Fusion Protein

TCGA All Mutated Fusion Protein Sequences

Fusion Protein ID

Sample ID

Mutated Partner

AAchange in WT

Seq. Length

AAchange in Fusion

CCLE All Mutated Fusion Protein Sequences

Fusion Protein ID

Sample ID

Mutated Partner

AAchange in WT

Seq. Length

AAchange in Fusion

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Fusion Gene Exprssed Samples for CMTR1_ZFAND3

RNA-seq based fusion gene expressed samples.

Source	Study	Disease	Sample	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
ChimerDB		THCA	TCGA-DE-A4MA-01A	CMTR1	chr6	37445415	+	ZFAND3	chr6	37445415	+
WashU		THCA	TCGA-DE-A4MA-01A	CMTR1	chr6	37445415	+	ZFAND3	chr6	38120011	+
cBioPortal	THCA_TCGA_PAN_CAN_ATLAS_2018	THPA	TCGA-DE-A4MA-01	CMTR1	chr6	37477639		ZFAND3	chr6	38152235

DNA-seq based fusion gene expressed samples.

Source

Study

Disease

Sample

Hgene

Hchr

Hbp

Hstrand

Tgene

Tchr

Tbp

Tstrand

SV type

dbVar

nstd151

Unknown_Cell

CMTR1

chr6

37446182

ZFAND3

chr6

38084520

DEL

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Related Drugs for CMTR1_ZFAND3

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.

PMID

Fusion Gene Name

Drug

Study Title

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

Partner

Gene

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status