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Center for Computational Systems Medicine level3
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein Structure

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pLDDT scores

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Ramachandran Plot of Fusion Protein Structure

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Potential Active Site Information

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Potentially Interacting Small Molecules through Virtual Screening

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Biochemical Features of Small Molecules with ADME

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Drug Toxicity Information

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:FHIT-HMGA2

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: FHIT-HMGA2
FusionPDB ID: 30354
FusionGDB2.0 ID: 30354
HgeneTgene
Gene symbol

FHIT

HMGA2

Gene ID

2272

8091

Gene namefragile histidine triad diadenosine triphosphatasehigh mobility group AT-hook 2
SynonymsAP3Aase|FRA3BBABL|HMGI-C|HMGIC|LIPO|STQTL9
Cytomap

3p14.2

12q14.3

Type of geneprotein-codingprotein-coding
Descriptionbis(5'-adenosyl)-triphosphataseAP3A hydrolasediadenosine 5',5'''-P1,P3-triphosphate hydrolasedinucleosidetriphosphatasehigh mobility group protein HMGI-CHMGA2/KRT121P fusionhigh-mobility group (nonhistone chromosomal) protein isoform I-C
Modification date2020031320200329
UniProtAcc

P49789

P52926

Ensembl transtripts involved in fusion geneENST idsENST00000476844, ENST00000492590, 
ENST00000341848, ENST00000466788, 
ENST00000468189, 
ENST00000393577, 
ENST00000403681, ENST00000541363, 
ENST00000354636, ENST00000536545, 
ENST00000393578, ENST00000425208, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score26 X 19 X 9=444616 X 12 X 5=960
# samples 2615
** MAII scorelog2(26/4446*10)=-4.09592441999854
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(15/960*10)=-2.67807190511264
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: FHIT [Title/Abstract] AND HMGA2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)
Anticipated loss of major functional domain due to fusion event.FHIT-HMGA2 seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
FHIT-HMGA2 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
FHIT-HMGA2 seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted ORF.
FHIT-HMGA2 seems lost the major protein functional domain in Tgene partner, which is a CGC due to the frame-shifted ORF.
FHIT-HMGA2 seems lost the major protein functional domain in Tgene partner, which is a transcription factor due to the frame-shifted ORF.
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

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

GO:0006163

purine nucleotide metabolic process

9323207

TgeneHMGA2

GO:0000122

negative regulation of transcription by RNA polymerase II

14627817

TgeneHMGA2

GO:0002062

chondrocyte differentiation

21484705

TgeneHMGA2

GO:0006284

base-excision repair

19465398

TgeneHMGA2

GO:0007095

mitotic G2 DNA damage checkpoint

16061642

TgeneHMGA2

GO:0010564

regulation of cell cycle process

14645522

TgeneHMGA2

GO:0010628

positive regulation of gene expression

18832382

TgeneHMGA2

GO:0031052

chromosome breakage

19549901

TgeneHMGA2

GO:0031507

heterochromatin assembly

16901784

TgeneHMGA2

GO:0035978

histone H2A-S139 phosphorylation

16061642

TgeneHMGA2

GO:0035986

senescence-associated heterochromatin focus assembly

16901784

TgeneHMGA2

GO:0035988

chondrocyte proliferation

21484705

TgeneHMGA2

GO:0042769

DNA damage response, detection of DNA damage

19465398

TgeneHMGA2

GO:0043065

positive regulation of apoptotic process

16061642

TgeneHMGA2

GO:0043066

negative regulation of apoptotic process

19465398

TgeneHMGA2

GO:0043392

negative regulation of DNA binding

14645522

TgeneHMGA2

GO:0043922

negative regulation by host of viral transcription

17005673

TgeneHMGA2

GO:0045869

negative regulation of single stranded viral RNA replication via double stranded DNA intermediate

17005673

TgeneHMGA2

GO:0045892

negative regulation of transcription, DNA-templated

18832382

TgeneHMGA2

GO:0045893

positive regulation of transcription, DNA-templated

15225648|15755872|17005673|17324944|17426251

TgeneHMGA2

GO:0045944

positive regulation of transcription by RNA polymerase II

14645522|18832382

TgeneHMGA2

GO:0071158

positive regulation of cell cycle arrest

16061642

TgeneHMGA2

GO:0071902

positive regulation of protein serine/threonine kinase activity

19549901

TgeneHMGA2

GO:0090402

oncogene-induced cell senescence

16901784

TgeneHMGA2

GO:2000648

positive regulation of stem cell proliferation

21484705

TgeneHMGA2

GO:2000679

positive regulation of transcription regulatory region DNA binding

18832382

TgeneHMGA2

GO:2000685

positive regulation of cellular response to X-ray

16061642

TgeneHMGA2

GO:2001022

positive regulation of response to DNA damage stimulus

16061642|19465398

TgeneHMGA2

GO:2001033

negative regulation of double-strand break repair via nonhomologous end joining

19549901

TgeneHMGA2

GO:2001038

regulation of cellular response to drug

16061642


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

check buttonFusion gene breakpoints across HMGA2 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.


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Fusion Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
check button Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0)
* All genome coordinats were lifted-over on hg19.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChimerKB3..FHITchr3

59737946

-HMGA2chr12

66308838

+
ChimerKB3..FHITchr3

59737946

-HMGA2chr12

66345162

+


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Fusion ORF Analysis


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)
BP loci
(transcript)
Predicted start
(transcript)
Predicted stop
(transcript)
Seq length
(amino acids)
ENST00000341848FHITchr359737946-ENST00000403681HMGA2chr1266345162+35284440443147
ENST00000341848FHITchr359737946-ENST00000393577HMGA2chr1266345162+6584440443147

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.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score

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Fusion Amino Acid Sequences


check button For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>30354_30354_1_FHIT-HMGA2_FHIT_chr3_59737946_ENST00000341848_HMGA2_chr12_66345162_ENST00000393577_length(amino acids)=147AA_BP=
MSFRFGQHLIKPSVVFLKTELSFALVNRKPVVPGHVLVCPLRPVERFHDLRPDEVADLFQTTQRVGTVVEKHFHGTSLTFSMQDGPEAGQ

--------------------------------------------------------------

>30354_30354_2_FHIT-HMGA2_FHIT_chr3_59737946_ENST00000341848_HMGA2_chr12_66345162_ENST00000403681_length(amino acids)=147AA_BP=
MSFRFGQHLIKPSVVFLKTELSFALVNRKPVVPGHVLVCPLRPVERFHDLRPDEVADLFQTTQRVGTVVEKHFHGTSLTFSMQDGPEAGQ

--------------------------------------------------------------

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Fusion Protein Functional Features


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr3:/chr12:)
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
- How to search
1. Put your fusion gene symbol.
2. Press the tab key until there will be shown the breakpoint information filled.
4. Go down and press 'Search' tab twice.
4. Go down to have the hyperlink of the search result.
5. Click the hyperlink.
6. See the FGviewer result for your fusion gene.
FGviewer

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

P49789

HMGA2

P52926

FUNCTION: Possesses dinucleoside triphosphate hydrolase activity (PubMed:12574506, PubMed:15182206, PubMed:8794732, PubMed:9323207, PubMed:9576908, PubMed:9543008). Cleaves P(1)-P(3)-bis(5'-adenosyl) triphosphate (Ap3A) to yield AMP and ADP (PubMed:12574506, PubMed:15182206, PubMed:8794732, PubMed:9323207, PubMed:9576908, PubMed:9543008). Can also hydrolyze P(1)-P(4)-bis(5'-adenosyl) tetraphosphate (Ap4A), but has extremely low activity with ATP (PubMed:8794732). Exhibits adenylylsulfatase activity, hydrolyzing adenosine 5'-phosphosulfate to yield AMP and sulfate (PubMed:18694747). Exhibits adenosine 5'-monophosphoramidase activity, hydrolyzing purine nucleotide phosphoramidates with a single phosphate group such as adenosine 5'monophosphoramidate (AMP-NH2) to yield AMP and NH2 (PubMed:18694747). Exhibits adenylylsulfate-ammonia adenylyltransferase, catalyzing the ammonolysis of adenosine 5'-phosphosulfate resulting in the formation of adenosine 5'-phosphoramidate (PubMed:26181368). Also catalyzes the ammonolysis of adenosine 5-phosphorofluoridate and diadenosine triphosphate (PubMed:26181368). Modulates transcriptional activation by CTNNB1 and thereby contributes to regulate the expression of genes essential for cell proliferation and survival, such as CCND1 and BIRC5 (PubMed:18077326). Plays a role in the induction of apoptosis via SRC and AKT1 signaling pathways (PubMed:16407838). Inhibits MDM2-mediated proteasomal degradation of p53/TP53 and thereby plays a role in p53/TP53-mediated apoptosis (PubMed:15313915). Induction of apoptosis depends on the ability of FHIT to bind P(1)-P(3)-bis(5'-adenosyl) triphosphate or related compounds, but does not require its catalytic activity, it may in part come from the mitochondrial form, which sensitizes the low-affinity Ca(2+) transporters, enhancing mitochondrial calcium uptake (PubMed:12574506, PubMed:19622739). Functions as tumor suppressor (By similarity). {ECO:0000250|UniProtKB:O89106, ECO:0000269|PubMed:12574506, ECO:0000269|PubMed:15313915, ECO:0000269|PubMed:16407838, ECO:0000269|PubMed:18077326, ECO:0000269|PubMed:18694747, ECO:0000269|PubMed:19622739, ECO:0000269|PubMed:26181368, ECO:0000269|PubMed:8794732, ECO:0000269|PubMed:9323207, ECO:0000269|PubMed:9543008}.FUNCTION: Functions as a transcriptional regulator. Functions in cell cycle regulation through CCNA2. Plays an important role in chromosome condensation during the meiotic G2/M transition of spermatocytes. Plays a role in postnatal myogenesis, is involved in satellite cell activation (By similarity). Positively regulates IGF2 expression through PLAG1 and in a PLAG1-independent manner (PubMed:28796236). {ECO:0000250|UniProtKB:P52927, ECO:0000269|PubMed:14645522, ECO:0000269|PubMed:28796236}.

check buttonRetention 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.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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Fusion Protein Structures

check button PDB and CIF files of the predicted fusion proteins
* Here we show the 3D structure of the fusion proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format.
Fusion protein PDB link (fusion AA seq ID in FusionPDB)HgeneHchrHbpHstrandTgeneTchrTbpTstrandAA seqLen(AA seq)
PDB file (9) >>>9.pdbFusion protein BP residue:
CIF file (9) >>>9.cif
FHITchr359737946-HMGA2chr1266345162+
MSFRFGQHLIKPSVVFLKTELSFALVNRKPVVPGHVLVCPLRPVERFHDL
RPDEVADLFQTTQRVGTVVEKHFHGTSLTFSMQDGPEAGQTVKHVHVHVL
147
3D view using mol* of 9 (AA BP:)


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pLDDT score distribution

check button pLDDT score distribution of the predicted wild-type structures of two partner proteins from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.
FHIT_pLDDT.png
all structure
all structure
HMGA2_pLDDT.png
all structure
all structure

check button pLDDT score distribution of the predicted fusion protein structures from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.
FHIT_HMGA2_9_pLDDT.png (AA BP:)
all structure
FHIT_HMGA2_9_pLDDT_and_active_sites.png (AA BP:)
all structure
FHIT_HMGA2_9_violinplot.png (AA BP:)
all structure


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Ramachandran Plot of Fusion Protein Structure


check button Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this fusion protein peptide.
Fusion AA seq ID in FusionPDB and their Ramachandran plots
FHIT_HMGA2_9.png
all structure

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Potential Active Site Information


check button The potential binding sites of these fusion proteins were identified using SiteMap, a module of the Schrodinger suite.
Fusion AA seq ID in FusionPDBSite scoreSizeD scoreVolumeExposureEnclosureContactPhobicPhilicBalanceDon/AccResidues
91.0361311.058336.8260.4820.7380.9780.9130.9970.9150.557Chain A: 5,8,9,10,11,13,14,25,26,27,28,29,37,83,90
,91,92,96,98,120,121,124,129,130,131,132,135

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Potentially Interacting Small Molecules through Virtual Screening


check button The FDA-approved small molecule library molecules were subjected to virtual screening using the Glide.
Fusion AA seq ID in FusionPDBZINC IDDrugBank IDDrug nameDocking scoreGlide gscore

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check button Drug information from DrugBank of the top 20 interacting small molecules.
ZINC IDDrugBank IDDrug nameDrug typeSMILESDrug group

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Biochemical Features of Small Molecules


check button ADME (Absorption, Distribution, Metabolism, and Excretion) of drugs using QikProp(v3.9)
ZINC IDmol_MWdipoleSASAFOSAFISAPISAWPSAvolumedonorHBaccptHBIPHuman Oral AbsorptionPercent Human Oral AbsorptionRule Of FiveRule Of Three


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Drug Toxicity Information


check button Toxicity information of individual drugs using eToxPred
ZINC IDSmileSurface AccessibilityToxicity


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Fusion Protein-Protein Interaction


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page.


check button Protein-protein interactors with each fusion partner protein in wild-type from validated records (BIOGRID-3.4.160)
GenePPI interactors
FHITFHIT, UBE2I, CTNNB1, LEF1, TRIM23, RAB40B, MDM2, REL, TP53, ARHGAP19, MTMR6, RABL2A, CHEK1, DDIT4L, SPERT, FDCSP, GAST, GGH, BCAS2, PRPF6, YTHDF1, Rbm14,
HMGA2RELA, NFKB1, PIAS3, RB1, PRMT6, NPM1, SMAD1, SMAD5, SMAD9, PRKCA, HDGF, PTBP1, APEX1, SYNCRIP, XRCC6, PSIP1, PA2G4, PCBP2, E4F1, OBSL1, HIST1H3A, CREB1, NFATC1, PCGF1, POU5F1, DLST, EZH2, SUZ12, MYC, TP53, MDM2, CSK, VRK1, HIST1H1B, PRKAG2, DUX4, DUX4L9, SYDE1, ARHGAP21, ARHGAP39, Plekhg5, ZNF263, MAFB, KAT2B, HIST1H2BG, LMNB1, NDUFAF7, CSNK2A1, LIG3, SUPT16H, VRK3, SP2, C1QBP, PARP2, TOP3A, CSNK2A2, XPC, RANBP17, PARP1, SUPV3L1, HIST2H2AC, HIST2H3PS2, KPNA4, USP7,


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
FHITall structure
HMGA2all structure


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs to FHIT-HMGA2


check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

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Related Diseases to FHIT-HMGA2


check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneFHITC0024121Lung Neoplasms2CTD_human
HgeneFHITC0025500Mesothelioma2CTD_human
HgeneFHITC0242379Malignant neoplasm of lung2CTD_human
HgeneFHITC0007097Carcinoma1CTD_human
HgeneFHITC0007131Non-Small Cell Lung Carcinoma1CTD_human
HgeneFHITC0013146Drug abuse1CTD_human
HgeneFHITC0013170Drug habituation1CTD_human
HgeneFHITC0013222Drug Use Disorders1CTD_human
HgeneFHITC0023903Liver neoplasms1CTD_human
HgeneFHITC0024623Malignant neoplasm of stomach1CTD_human
HgeneFHITC0029231Organic Mental Disorders, Substance-Induced1CTD_human
HgeneFHITC0033578Prostatic Neoplasms1CTD_human
HgeneFHITC0038356Stomach Neoplasms1CTD_human
HgeneFHITC0038580Substance Dependence1CTD_human
HgeneFHITC0038586Substance Use Disorders1CTD_human
HgeneFHITC0042076Urologic Neoplasms1CTD_human
HgeneFHITC0205696Anaplastic carcinoma1CTD_human
HgeneFHITC0205697Carcinoma, Spindle-Cell1CTD_human
HgeneFHITC0205698Undifferentiated carcinoma1CTD_human
HgeneFHITC0205699Carcinomatosis1CTD_human
HgeneFHITC0236733Amphetamine-Related Disorders1CTD_human
HgeneFHITC0236804Amphetamine Addiction1CTD_human
HgeneFHITC0236807Amphetamine Abuse1CTD_human
HgeneFHITC0236969Substance-Related Disorders1CTD_human
HgeneFHITC0345904Malignant neoplasm of liver1CTD_human
HgeneFHITC0376358Malignant neoplasm of prostate1CTD_human
HgeneFHITC0740858Substance abuse problem1CTD_human
HgeneFHITC0751571Cancer of Urinary Tract1CTD_human
HgeneFHITC1510472Drug Dependence1CTD_human
HgeneFHITC1708349Hereditary Diffuse Gastric Cancer1CTD_human
HgeneFHITC4316881Prescription Drug Abuse1CTD_human
TgeneHMGA2C1519176Salivary Gland Pleomorphic Adenoma2ORPHANET
TgeneHMGA2C0005612Birth Weight1CTD_human
TgeneHMGA2C0006826Malignant Neoplasms1CTD_human
TgeneHMGA2C0027626Neoplasm Invasiveness1CTD_human
TgeneHMGA2C0027651Neoplasms1CTD_human
TgeneHMGA2C0086692Benign Neoplasm1CTD_human
TgeneHMGA2C0175693Russell-Silver syndrome1GENOMICS_ENGLAND
TgeneHMGA2C0473935Radiolabeled somatostatin analog study1GENOMICS_ENGLAND
TgeneHMGA2C0796160MENTAL RETARDATION, X-LINKED, SNYDER-ROBINSON TYPE1GENOMICS_ENGLAND
TgeneHMGA2C1096309Myolipoma1GENOMICS_ENGLAND
TgeneHMGA2C430514012q14 microdeletion syndrome1ORPHANET