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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:STK39_MAT1A (FusionGDB2 ID:HG27347TG4143)

Fusion Gene Summary for STK39_MAT1A

Fusion gene summary

Fusion gene information	Fusion gene name: STK39_MAT1A
	Fusion gene ID: hg27347tg4143
		Hgene	Tgene
	Gene symbol	STK39	MAT1A
	Gene ID	27347	4143
	Gene name	serine/threonine kinase 39	methionine adenosyltransferase 1A
	Synonyms	DCHT|PASK|SPAK	MAT|MATA1|SAMS|SAMS1
	Cytomap	2q24.3	10q22.3
	Type of gene	protein-coding	protein-coding
	Description	STE20/SPS1-related proline-alanine-rich protein kinaseSTE20/SPS1 homologSte20-like protein kinaseproline-alanine-rich STE20-related kinaseserine threonine kinase 39 (STE20/SPS1 homolog, yeast)serine/threonine-protein kinase 39small intestine SPAK-li	S-adenosylmethionine synthase isoform type-1MAT 1MAT-I/IIIadoMet synthase 1adoMet synthetase 1methionine adenosyltransferase 1methionine adenosyltransferase I, alphamethionine adenosyltransferase I/III
	Modification date	20240411	20240305
	UniProtAcc	.	.
	Ensembl transtripts involved in fusion gene	ENST00000355999, ENST00000487143,
Fusion gene scores	* DoF score	* DoF score (Degree of Frequency) = # partners X # break points X # disease types 17 X 22 X 14=5236	* DoF score (Degree of Frequency) = # partners X # break points X # disease types 3 X 4 X 4=48
	# samples	28	25
	** MAII score	** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10) log2(28/5236*10)=-4.22496636500027 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(25/48*10)=2.38082178394093 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0
Context	PubMed: STK39 [Title/Abstract] AND MAT1A [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint	STK39(168931491)-MAT1A(82045345), # samples:1

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Fusion Gene Breakpoints for STK39_MAT1A

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 STK39_MAT1A

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	STK39	GO:0006884	cell volume homeostasis	36318922
Hgene	STK39	GO:0007165	signal transduction	24393035
Hgene	STK39	GO:0018105	peptidyl-serine phosphorylation	24393035
Hgene	STK39	GO:0018107	peptidyl-threonine phosphorylation	24393035
Hgene	STK39	GO:0035556	intracellular signal transduction	24393035
Hgene	STK39	GO:0070294	renal sodium ion absorption	18270262
Hgene	STK39	GO:0071474	cellular hyperosmotic response	36318922
Hgene	STK39	GO:0071476	cellular hypotonic response	24393035
Hgene	STK39	GO:1901017	negative regulation of potassium ion transmembrane transporter activity	24393035
Hgene	STK39	GO:1901380	negative regulation of potassium ion transmembrane transport	24393035
Hgene	STK39	GO:1905408	negative regulation of creatine transmembrane transporter activity	25531585
Hgene	STK39	GO:2000650	negative regulation of sodium ion transmembrane transporter activity	25531585
Tgene	MAT1A	GO:0006556	S-adenosylmethionine biosynthetic process	25075345
Tgene	MAT1A	GO:0051289	protein homotetramerization	23425511

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Fusion Genomic Features for STK39_MAT1A

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)
STK39	chr2	168931491	-	MAT1A	chr10	82045345	-	7.40e-09	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 STK39_MAT1A

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 STK39_MAT1A

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 STK39_MAT1A

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 STK39_MAT1A

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 STK39_MAT1A

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 STK39_MAT1A

RNA-seq based fusion gene expressed samples.

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Related Drugs for STK39_MAT1A

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)