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Center for Computational Systems Medicine level1
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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-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:TCF12-NIPA1

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: TCF12-NIPA1
FusionPDB ID: 89714
FusionGDB2.0 ID: 89714
HgeneTgene
Gene symbol

TCF12

NIPA1

Gene ID

6938

123606

Gene nametranscription factor 12NIPA magnesium transporter 1
SynonymsCRS3|HEB|HTF4|HsT17266|TCF-12|bHLHb20|p64FSP3|SLC57A1|SPG6
Cytomap

15q21.3

15q11.2

Type of geneprotein-codingprotein-coding
Descriptiontranscription factor 12DNA-binding protein HTF4E-box-binding proteinclass B basic helix-loop-helix protein 20helix-loop-helix transcription factor 4transcription factor HTF-4magnesium transporter NIPA1non imprinted in Prader-Willi/Angelman syndrome 1non-imprinted in Prader-Willi/Angelman syndrome region protein 1spastic paraplegia 6 protein
Modification date2020031320200313
UniProtAcc.

Q7RTP0

Ensembl transtripts involved in fusion geneENST idsENST00000267811, ENST00000333725, 
ENST00000438423, ENST00000452095, 
ENST00000557843, ENST00000343827, 
ENST00000537840, ENST00000543579, 
ENST00000559703, ENST00000559710, 
ENST00000560764, 		ENST00000437912, 
ENST00000538684, ENST00000561183, 
ENST00000337435, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score29 X 19 X 12=66121 X 1 X 1=1
# samples 321
** MAII scorelog2(32/6612*10)=-4.36894291440495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(1/1*10)=3.32192809488736
Context (manual curation of fusion genes in FusionPDB)

PubMed: TCF12 [Title/Abstract] AND NIPA1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)TCF12(57213296)-NIPA1(23062319), # samples:2
Anticipated loss of major functional domain due to fusion event.TCF12-NIPA1 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
TCF12-NIPA1 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
TCF12-NIPA1 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
TCF12-NIPA1 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame 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
HgeneTCF12

GO:0045944

positive regulation of transcription by RNA polymerase II

11802795


check buttonFusion gene breakpoints across TCF12 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check buttonFusion gene breakpoints across NIPA1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


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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
ChimerDB4LUADTCGA-75-7031-01ATCF12chr15

57213296

+NIPA1chr15

23062319

-
ChimerDB4LUADTCGA-75-7031-01ATCF12chr15

57213296

+NIPA1chr15

23062319

+


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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)
ENST00000438423TCF12chr1557213296+ENST00000337435NIPA1chr1523062319+68084442601255331
ENST00000267811TCF12chr1557213296+ENST00000337435NIPA1chr1523062319+68164523041263319
ENST00000452095TCF12chr1557213296+ENST00000337435NIPA1chr1523062319+68064422941253319
ENST00000333725TCF12chr1557213296+ENST00000337435NIPA1chr1523062319+67473832351194319
ENST00000557843TCF12chr1557213296+ENST00000337435NIPA1chr1523062319+6599235511046331

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
ENST00000438423ENST00000337435TCF12chr1557213296+NIPA1chr1523062319+0.0003394570.9996605
ENST00000267811ENST00000337435TCF12chr1557213296+NIPA1chr1523062319+0.0003400190.99966
ENST00000452095ENST00000337435TCF12chr1557213296+NIPA1chr1523062319+0.0003389740.9996611
ENST00000333725ENST00000337435TCF12chr1557213296+NIPA1chr1523062319+0.0003286020.99967146
ENST00000557843ENST00000337435TCF12chr1557213296+NIPA1chr1523062319+0.0003057260.99969435

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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

>89714_89714_1_TCF12-NIPA1_TCF12_chr15_57213296_ENST00000267811_NIPA1_chr15_23062319_ENST00000337435_length(amino acids)=319AA_BP=49
MNPQQQRMAAIGTDKELSDLLDFSAMFSPPVNSGKTRPTTLGSSQFSGSGTSYLTDIVWWAGTIAMAVGQIGNFLAYTAVPTVLVTPLGA
LGVPFGSILASYLLKEKLNILGKLGCLLSCAGSVVLIIHSPKSESVTTQAELEEKLTNPVFVGYLCIVLLMLLLLIFWIAPAHGPTNIMV
YISICSLLGSFTVPSTKGIGLAAQDILHNNPSSQRALCLCLVLLAVLGCSIIVQFRYINKALECFDSSVFGAIYYVVFTTLVLLASAILF

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

>89714_89714_2_TCF12-NIPA1_TCF12_chr15_57213296_ENST00000333725_NIPA1_chr15_23062319_ENST00000337435_length(amino acids)=319AA_BP=49
MNPQQQRMAAIGTDKELSDLLDFSAMFSPPVNSGKTRPTTLGSSQFSGSGTSYLTDIVWWAGTIAMAVGQIGNFLAYTAVPTVLVTPLGA
LGVPFGSILASYLLKEKLNILGKLGCLLSCAGSVVLIIHSPKSESVTTQAELEEKLTNPVFVGYLCIVLLMLLLLIFWIAPAHGPTNIMV
YISICSLLGSFTVPSTKGIGLAAQDILHNNPSSQRALCLCLVLLAVLGCSIIVQFRYINKALECFDSSVFGAIYYVVFTTLVLLASAILF

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

>89714_89714_3_TCF12-NIPA1_TCF12_chr15_57213296_ENST00000438423_NIPA1_chr15_23062319_ENST00000337435_length(amino acids)=331AA_BP=61
MDAETGRQKWPKMNPQQQRMAAIGTDKELSDLLDFSAMFSPPVNSGKTRPTTLGSSQFSGSGTSYLTDIVWWAGTIAMAVGQIGNFLAYT
AVPTVLVTPLGALGVPFGSILASYLLKEKLNILGKLGCLLSCAGSVVLIIHSPKSESVTTQAELEEKLTNPVFVGYLCIVLLMLLLLIFW
IAPAHGPTNIMVYISICSLLGSFTVPSTKGIGLAAQDILHNNPSSQRALCLCLVLLAVLGCSIIVQFRYINKALECFDSSVFGAIYYVVF

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

>89714_89714_4_TCF12-NIPA1_TCF12_chr15_57213296_ENST00000452095_NIPA1_chr15_23062319_ENST00000337435_length(amino acids)=319AA_BP=49
MNPQQQRMAAIGTDKELSDLLDFSAMFSPPVNSGKTRPTTLGSSQFSGSGTSYLTDIVWWAGTIAMAVGQIGNFLAYTAVPTVLVTPLGA
LGVPFGSILASYLLKEKLNILGKLGCLLSCAGSVVLIIHSPKSESVTTQAELEEKLTNPVFVGYLCIVLLMLLLLIFWIAPAHGPTNIMV
YISICSLLGSFTVPSTKGIGLAAQDILHNNPSSQRALCLCLVLLAVLGCSIIVQFRYINKALECFDSSVFGAIYYVVFTTLVLLASAILF

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

>89714_89714_5_TCF12-NIPA1_TCF12_chr15_57213296_ENST00000557843_NIPA1_chr15_23062319_ENST00000337435_length(amino acids)=331AA_BP=61
MDAETGRQKWPKMNPQQQRMAAIGTDKELSDLLDFSAMFSPPVNSGKTRPTTLGSSQFSGSGTSYLTDIVWWAGTIAMAVGQIGNFLAYT
AVPTVLVTPLGALGVPFGSILASYLLKEKLNILGKLGCLLSCAGSVVLIIHSPKSESVTTQAELEEKLTNPVFVGYLCIVLLMLLLLIFW
IAPAHGPTNIMVYISICSLLGSFTVPSTKGIGLAAQDILHNNPSSQRALCLCLVLLAVLGCSIIVQFRYINKALECFDSSVFGAIYYVVF

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

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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/chr15:57213296/chr15:23062319)
- 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
.NIPA1

Q7RTP0

FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.FUNCTION: Acts as a Mg(2+) transporter. Can also transport other divalent cations such as Fe(2+), Sr(2+), Ba(2+), Mn(2+) and Co(2+) but to a much less extent than Mg(2+) (By similarity). {ECO:0000250}.

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
HgeneTCF12chr15:57213296chr15:23062319ENST00000267811+32019_2749.3333333333333361821.3333333333333MotifNote=9aaTAD
HgeneTCF12chr15:57213296chr15:23062319ENST00000333725+32119_2749.3333333333333361420.0MotifNote=9aaTAD
HgeneTCF12chr15:57213296chr15:23062319ENST00000438423+32119_2749.3333333333333361398.3333333333333MotifNote=9aaTAD
HgeneTCF12chr15:57213296chr15:23062319ENST00000557843+32019_2749.3333333333333361301.0MotifNote=9aaTAD
TgeneNIPA1chr15:57213296chr15:23062319ENST0000033743505110_11759.333333333333336330.0Topological domainCytoplasmic
TgeneNIPA1chr15:57213296chr15:23062319ENST0000033743505139_15959.333333333333336330.0Topological domainExtracellular
TgeneNIPA1chr15:57213296chr15:23062319ENST0000033743505181_18359.333333333333336330.0Topological domainCytoplasmic
TgeneNIPA1chr15:57213296chr15:23062319ENST0000033743505205_22459.333333333333336330.0Topological domainExtracellular
TgeneNIPA1chr15:57213296chr15:23062319ENST0000033743505246_25959.333333333333336330.0Topological domainCytoplasmic
TgeneNIPA1chr15:57213296chr15:23062319ENST0000033743505281_29059.333333333333336330.0Topological domainExtracellular
TgeneNIPA1chr15:57213296chr15:23062319ENST0000033743505312_32959.333333333333336330.0Topological domainCytoplasmic
TgeneNIPA1chr15:57213296chr15:23062319ENST000003374350588_8859.333333333333336330.0Topological domainExtracellular
TgeneNIPA1chr15:57213296chr15:23062319ENST0000043791205110_1170255.0Topological domainCytoplasmic
TgeneNIPA1chr15:57213296chr15:23062319ENST0000043791205139_1590255.0Topological domainExtracellular
TgeneNIPA1chr15:57213296chr15:23062319ENST0000043791205181_1830255.0Topological domainCytoplasmic
TgeneNIPA1chr15:57213296chr15:23062319ENST00000437912051_270255.0Topological domainExtracellular
TgeneNIPA1chr15:57213296chr15:23062319ENST0000043791205205_2240255.0Topological domainExtracellular
TgeneNIPA1chr15:57213296chr15:23062319ENST0000043791205246_2590255.0Topological domainCytoplasmic
TgeneNIPA1chr15:57213296chr15:23062319ENST0000043791205281_2900255.0Topological domainExtracellular
TgeneNIPA1chr15:57213296chr15:23062319ENST0000043791205312_3290255.0Topological domainCytoplasmic
TgeneNIPA1chr15:57213296chr15:23062319ENST000004379120549_660255.0Topological domainCytoplasmic
TgeneNIPA1chr15:57213296chr15:23062319ENST000004379120588_880255.0Topological domainExtracellular
TgeneNIPA1chr15:57213296chr15:23062319ENST0000056118305110_1170255.0Topological domainCytoplasmic
TgeneNIPA1chr15:57213296chr15:23062319ENST0000056118305139_1590255.0Topological domainExtracellular
TgeneNIPA1chr15:57213296chr15:23062319ENST0000056118305181_1830255.0Topological domainCytoplasmic
TgeneNIPA1chr15:57213296chr15:23062319ENST00000561183051_270255.0Topological domainExtracellular
TgeneNIPA1chr15:57213296chr15:23062319ENST0000056118305205_2240255.0Topological domainExtracellular
TgeneNIPA1chr15:57213296chr15:23062319ENST0000056118305246_2590255.0Topological domainCytoplasmic
TgeneNIPA1chr15:57213296chr15:23062319ENST0000056118305281_2900255.0Topological domainExtracellular
TgeneNIPA1chr15:57213296chr15:23062319ENST0000056118305312_3290255.0Topological domainCytoplasmic
TgeneNIPA1chr15:57213296chr15:23062319ENST000005611830549_660255.0Topological domainCytoplasmic
TgeneNIPA1chr15:57213296chr15:23062319ENST000005611830588_880255.0Topological domainExtracellular
TgeneNIPA1chr15:57213296chr15:23062319ENST0000033743505118_13859.333333333333336330.0TransmembraneHelical
TgeneNIPA1chr15:57213296chr15:23062319ENST0000033743505160_18059.333333333333336330.0TransmembraneHelical
TgeneNIPA1chr15:57213296chr15:23062319ENST0000033743505184_20459.333333333333336330.0TransmembraneHelical
TgeneNIPA1chr15:57213296chr15:23062319ENST0000033743505225_24559.333333333333336330.0TransmembraneHelical
TgeneNIPA1chr15:57213296chr15:23062319ENST0000033743505260_28059.333333333333336330.0TransmembraneHelical
TgeneNIPA1chr15:57213296chr15:23062319ENST0000033743505291_31159.333333333333336330.0TransmembraneHelical
TgeneNIPA1chr15:57213296chr15:23062319ENST000003374350567_8759.333333333333336330.0TransmembraneHelical
TgeneNIPA1chr15:57213296chr15:23062319ENST000003374350589_10959.333333333333336330.0TransmembraneHelical
TgeneNIPA1chr15:57213296chr15:23062319ENST0000043791205118_1380255.0TransmembraneHelical
TgeneNIPA1chr15:57213296chr15:23062319ENST0000043791205160_1800255.0TransmembraneHelical
TgeneNIPA1chr15:57213296chr15:23062319ENST0000043791205184_2040255.0TransmembraneHelical
TgeneNIPA1chr15:57213296chr15:23062319ENST0000043791205225_2450255.0TransmembraneHelical
TgeneNIPA1chr15:57213296chr15:23062319ENST0000043791205260_2800255.0TransmembraneHelical
TgeneNIPA1chr15:57213296chr15:23062319ENST000004379120528_480255.0TransmembraneHelical
TgeneNIPA1chr15:57213296chr15:23062319ENST0000043791205291_3110255.0TransmembraneHelical
TgeneNIPA1chr15:57213296chr15:23062319ENST000004379120567_870255.0TransmembraneHelical
TgeneNIPA1chr15:57213296chr15:23062319ENST000004379120589_1090255.0TransmembraneHelical
TgeneNIPA1chr15:57213296chr15:23062319ENST0000056118305118_1380255.0TransmembraneHelical
TgeneNIPA1chr15:57213296chr15:23062319ENST0000056118305160_1800255.0TransmembraneHelical
TgeneNIPA1chr15:57213296chr15:23062319ENST0000056118305184_2040255.0TransmembraneHelical
TgeneNIPA1chr15:57213296chr15:23062319ENST0000056118305225_2450255.0TransmembraneHelical
TgeneNIPA1chr15:57213296chr15:23062319ENST0000056118305260_2800255.0TransmembraneHelical
TgeneNIPA1chr15:57213296chr15:23062319ENST000005611830528_480255.0TransmembraneHelical
TgeneNIPA1chr15:57213296chr15:23062319ENST0000056118305291_3110255.0TransmembraneHelical
TgeneNIPA1chr15:57213296chr15:23062319ENST000005611830567_870255.0TransmembraneHelical
TgeneNIPA1chr15:57213296chr15:23062319ENST000005611830589_1090255.0TransmembraneHelical

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneTCF12chr15:57213296chr15:23062319ENST00000267811+320577_63049.3333333333333361821.3333333333333DomainbHLH
HgeneTCF12chr15:57213296chr15:23062319ENST00000333725+321577_63049.3333333333333361420.0DomainbHLH
HgeneTCF12chr15:57213296chr15:23062319ENST00000343827+113577_63001254.6666666666667DomainbHLH
HgeneTCF12chr15:57213296chr15:23062319ENST00000438423+321577_63049.3333333333333361398.3333333333333DomainbHLH
HgeneTCF12chr15:57213296chr15:23062319ENST00000557843+320577_63049.3333333333333361301.0DomainbHLH
HgeneTCF12chr15:57213296chr15:23062319ENST00000343827+11319_2701254.6666666666667MotifNote=9aaTAD
HgeneTCF12chr15:57213296chr15:23062319ENST00000267811+320119_14049.3333333333333361821.3333333333333RegionNote=Leucine-zipper
HgeneTCF12chr15:57213296chr15:23062319ENST00000267811+320632_65549.3333333333333361821.3333333333333RegionNote=Class A specific domain
HgeneTCF12chr15:57213296chr15:23062319ENST00000333725+321119_14049.3333333333333361420.0RegionNote=Leucine-zipper
HgeneTCF12chr15:57213296chr15:23062319ENST00000333725+321632_65549.3333333333333361420.0RegionNote=Class A specific domain
HgeneTCF12chr15:57213296chr15:23062319ENST00000343827+113119_14001254.6666666666667RegionNote=Leucine-zipper
HgeneTCF12chr15:57213296chr15:23062319ENST00000343827+113632_65501254.6666666666667RegionNote=Class A specific domain
HgeneTCF12chr15:57213296chr15:23062319ENST00000438423+321119_14049.3333333333333361398.3333333333333RegionNote=Leucine-zipper
HgeneTCF12chr15:57213296chr15:23062319ENST00000438423+321632_65549.3333333333333361398.3333333333333RegionNote=Class A specific domain
HgeneTCF12chr15:57213296chr15:23062319ENST00000557843+320119_14049.3333333333333361301.0RegionNote=Leucine-zipper
HgeneTCF12chr15:57213296chr15:23062319ENST00000557843+320632_65549.3333333333333361301.0RegionNote=Class A specific domain
TgeneNIPA1chr15:57213296chr15:23062319ENST00000337435051_2759.333333333333336330.0Topological domainExtracellular
TgeneNIPA1chr15:57213296chr15:23062319ENST000003374350549_6659.333333333333336330.0Topological domainCytoplasmic
TgeneNIPA1chr15:57213296chr15:23062319ENST000003374350528_4859.333333333333336330.0TransmembraneHelical


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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


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
TCF12
NIPA1


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
HgeneTCF12chr15:57213296chr15:23062319ENST00000267811+320182_19649.3333333333333361821.3333333333333RUNX1T1
HgeneTCF12chr15:57213296chr15:23062319ENST00000333725+321182_19649.3333333333333361420.0RUNX1T1
HgeneTCF12chr15:57213296chr15:23062319ENST00000343827+113182_19601254.6666666666667RUNX1T1
HgeneTCF12chr15:57213296chr15:23062319ENST00000438423+321182_19649.3333333333333361398.3333333333333RUNX1T1
HgeneTCF12chr15:57213296chr15:23062319ENST00000557843+320182_19649.3333333333333361301.0RUNX1T1


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Related Drugs to TCF12-NIPA1


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 TCF12-NIPA1


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