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Center for Computational Systems Medicine
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FusionGeneSummary

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FusionProtFeature

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FusionGeneSequence

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FusionGenePPI

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RelatedDrugs

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RelatedDiseases

Fusion gene ID: 30430

FusionGeneSummary for RAPGEF1_ZMYND19

check button Fusion gene summary
Fusion gene informationFusion gene name: RAPGEF1_ZMYND19
Fusion gene ID: 30430
HgeneTgene
Gene symbol

RAPGEF1

ZMYND19

Gene ID

2889

116225

Gene nameRap guanine nucleotide exchange factor 1zinc finger MYND-type containing 19
SynonymsC3G|GRF2MIZIP
Cytomap

9q34.13

9q34.3

Type of geneprotein-codingprotein-coding
Descriptionrap guanine nucleotide exchange factor 1CRK SH3-binding GNRPRap guanine nucleotide exchange factor (GEF) 1guanine nucleotide-releasing factor 2 (specific for crk proto-oncogene)zinc finger MYND domain-containing protein 19MCH-R1-interacting zinc finger proteinmelanin-concentrating hormone receptor 1 interacting zinc-finger proteinzinc finger, MYND domain containing 19
Modification date2018052220180522
UniProtAcc

Q13905

Q96E35

Ensembl transtripts involved in fusion geneENST00000372189, ENST00000372195, 
ENST00000372190, ENST00000481260, 
ENST00000298585, ENST00000471957, 
Fusion gene scores* DoF score17 X 14 X 10=23805 X 3 X 7=105
# samples 217
** MAII scorelog2(21/2380*10)=-3.50250034052918
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(7/105*10)=-0.584962500721156
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: RAPGEF1 [Title/Abstract] AND ZMYND19 [Title/Abstract] AND fusion [Title/Abstract]

Functional or gene categories assigned by FusionGDB annotation
* 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
HgeneRAPGEF1

GO:0038180

nerve growth factor signaling pathway

17724123

HgeneRAPGEF1

GO:0043547

positive regulation of GTPase activity

10548487

HgeneRAPGEF1

GO:0071320

cellular response to cAMP

21840392

HgeneRAPGEF1

GO:1990090

cellular response to nerve growth factor stimulus

17724123


check button Fusion gene information from three resources
(ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018))
* 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.
Data typeSourceCancer typeSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
TCGARVSKCMTCGA-WE-A8ZR-06ARAPGEF1chr9

134585007

-ZMYND19chr9

140483170

-
* LD: Li Ding group's fusion gene list
  RV: Roel Verhaak group's fusion gene list
  ChiTaRs fusion database

check button 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.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand
intron-3CDSENST00000372189ENST00000298585RAPGEF1chr9

134585007

-ZMYND19chr9

140483170

-
intron-5UTRENST00000372189ENST00000471957RAPGEF1chr9

134585007

-ZMYND19chr9

140483170

-
intron-3CDSENST00000372195ENST00000298585RAPGEF1chr9

134585007

-ZMYND19chr9

140483170

-
intron-5UTRENST00000372195ENST00000471957RAPGEF1chr9

134585007

-ZMYND19chr9

140483170

-
In-frameENST00000372190ENST00000298585RAPGEF1chr9

134585007

-ZMYND19chr9

140483170

-
5CDS-5UTRENST00000372190ENST00000471957RAPGEF1chr9

134585007

-ZMYND19chr9

140483170

-
intron-3CDSENST00000481260ENST00000298585RAPGEF1chr9

134585007

-ZMYND19chr9

140483170

-
intron-5UTRENST00000481260ENST00000471957RAPGEF1chr9

134585007

-ZMYND19chr9

140483170

-

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FusionProtFeatures for RAPGEF1_ZMYND19


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
RAPGEF1

Q13905

ZMYND19

Q96E35

Guanine nucleotide-releasing protein that binds to SH3domain of CRK and GRB2/ASH. Transduces signals from CRK toactivate RAS. Plays a role in the establishment of basalendothelial barrier function. Plays a role in nerve growth factor(NGF)-induced sustained activation of Rap1 and neurite outgrowth.{ECO:0000269|PubMed:17724123, ECO:0000269|PubMed:21840392,ECO:0000269|PubMed:7806500}. May be involved as a regulatory molecule in GPR24/MCH-R1signaling.

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.
- In-frame and retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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FusionGeneSequence for RAPGEF1_ZMYND19


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences.
(nt: nucleotides, aa: amino acids)

* Fusion amino acid sequences.
>In-frame_RAPGEF1_ENST00000372190_chr9_134585007_-_ZMYND19_ENST00000298585_chr9_140483170_-_232aa
MGNAIEKQKPLKRSHLYPWKQDQIHADR_AGHPAGGELLL_GPNGSGCRWKWC_DICLCL_QEPRKGLWETPS_AAVGAAPGGRGPGLPG
GAPQRCDRGQSPGQPATGAVGLAAQG_RDLQQAEGAKLVLACNSAAAYRPTRRTVSCPKCDPVL_CQRGCSGRGGELLHLL_VPLPSLHS


* Fusion transcript sequences (only coding sequence (CDS) region).
>In-frame_RAPGEF1_ENST00000372190_chr9_134585007_-_ZMYND19_ENST00000298585_chr9_140483170_-_697nt
ATGGGCAATGCTATTGAAAAACAGAAGCCCTTGAAACGAAGTCATCTGTACCCCTGGAAACAAGACCAAATACACGCTGATCGATGAGCA
GGACATCCCGCTGGTGGAGAGCTACTCCTTTGAGGCCCGAATGGAAGTGGATGCAGATGGAAATGGTGCTAAGATATTTGCCTATGCCTT
TGACAAGAACCGAGGAAGGGGCTCTGGGAGACTCCTTCATGAGCTGCTGTGGGAGCGGCACCGGGGGGGCGTGGCCCCGGGCTTCCAGGT
GGTGCACCTCAACGCTGTGACCGTGGACAATCGCCTGGACAACCTGCAACTGGTGCCGTGGGGCTGGCGGCCCAAGGCTGAAGAGACCTC
CAGCAAGCAGAGGGAGCAAAGCTTGTATTGGCTTGCAATTCAGCAGCTGCCTACAGACCCTATAGAAGAACAGTTTCCTGTCCTAAATGT
GACCCGGTATTATAATGCCAACGGGGATGTAGTGGAAGAGGAGGAGAACTCTTGCACCTACTATGAGTGCCACTACCCTCCCTGCACAGT
GATTGAGAAGCAGCTCCGGGAGTTCAACATCTGTGGGCGCTGCCAGGTGGCCCGGTACTGCGGCTCCCAGTGCCAGCAGAAGGACTGGCC


* Fusion transcript sequences (Full-length transcript).
>In-frame_RAPGEF1_ENST00000372190_chr9_134585007_-_ZMYND19_ENST00000298585_chr9_140483170_-_1320nt
GAGATTCCTCAGGCTTCCCTTGTGAGGCTGCCTGGGTTCTGCCGCTGGGTGGTTTGGGATGTCCAAGAGATATCCCCTTTCAGCCAGTGA
CTCGGTCCTCAGTTGCTGCTCCGGAAAGACGCTGGGGCTGGGAAGGGCCCTGTGTCCTCTGGCTTTAAAATGGGCAATGCTATTGAAAAA
CAGAAGCCCTTGAAACGAAGTCATCTGTACCCCTGGAAACAAGACCAAATACACGCTGATCGATGAGCAGGACATCCCGCTGGTGGAGAG
CTACTCCTTTGAGGCCCGAATGGAAGTGGATGCAGATGGAAATGGTGCTAAGATATTTGCCTATGCCTTTGACAAGAACCGAGGAAGGGG
CTCTGGGAGACTCCTTCATGAGCTGCTGTGGGAGCGGCACCGGGGGGGCGTGGCCCCGGGCTTCCAGGTGGTGCACCTCAACGCTGTGAC
CGTGGACAATCGCCTGGACAACCTGCAACTGGTGCCGTGGGGCTGGCGGCCCAAGGCTGAAGAGACCTCCAGCAAGCAGAGGGAGCAAAG
CTTGTATTGGCTTGCAATTCAGCAGCTGCCTACAGACCCTATAGAAGAACAGTTTCCTGTCCTAAATGTGACCCGGTATTATAATGCCAA
CGGGGATGTAGTGGAAGAGGAGGAGAACTCTTGCACCTACTATGAGTGCCACTACCCTCCCTGCACAGTGATTGAGAAGCAGCTCCGGGA
GTTCAACATCTGTGGGCGCTGCCAGGTGGCCCGGTACTGCGGCTCCCAGTGCCAGCAGAAGGACTGGCCTGCCCACAAGAAGCACTGTCG
GGAGAGGAAGCGTCCCTTCCAGCATGAGCTTGAGCCAGAGCGATGACGGGCAGGGGAGCCACACATACTCACAGCCCCCGGGCTCTACCC
TGGGCACAGCAGAGACAGACTGGTGGTTGAACCTGGAGGTGCCAAAAAAGCCAGCTGCGGGCCCAGGACAGCTGCCGTGAGACTCCCGAT
GTCACAGGCAGTCTGTGTGGTTACAGCGCCCCTCAGTGTTCATCTCCAGCAGAGACAACGGAGGAGGCTCCCACCAGGACGGTTCTCATT
ATTTATATGTTAATATGTTTGTAAACTCATGTACAGTTTTTTTTGGGGGGGAGGCAATGGGAAGGGTAGAAATTACAAATAGAATCATTT
GCTGTAATCCTTAAATGGCAAACGGTCAGGCCACGTGACTAAAAACTGTCCTGTTGTCGAAGCTTCTCCCCTGGGCCGCCGGGAGCCCCG


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FusionGenePPI for RAPGEF1_ZMYND19


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 (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors
RAPGEF1BCAR1, HCK, CRKL, NEDD9, GRB2, CRK, SHC1, CBL, ATXN1, MBIP, RPS15, SLC20A1, MOV10, NXF1, ABL1, EGFR, SPATS2L, RAP1A, RAP2BZMYND19PPP1R37, HACL1, KCTD13, TNNT1, ELAVL1, NAB2, TRIM27, TOX4, ENOX1, FIP1L1, LZTS2, PNMA5, FAM154A, SELV, INCA1, CCDC183, GLIPR1L2, TDGF1, MRPL4, RMND5A, MRPS30, PRG2, TNFAIP1, PRG3, TIGD5, PIGT, GABRA6, INSL6, NEU4, KRBA1, CDK5RAP1, SUCLA2, CCDC120, IKZF1, TLE4, NFATC1, BMP1, TMEM70, NDUFS6, MKLN1, ARMC8, RANBP9


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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RelatedDrugs for RAPGEF1_ZMYND19


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for RAPGEF1_ZMYND19


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource