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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: 1037

FusionGeneSummary for AFP_SMC1A

check button Fusion gene summary
Fusion gene informationFusion gene name: AFP_SMC1A
Fusion gene ID: 1037
HgeneTgene
Gene symbol

AFP

SMC1A

Gene ID

7726

8243

Gene nametripartite motif containing 26structural maintenance of chromosomes 1A
SynonymsAFP|RNF95|ZNF173CDLS2|DXS423E|SB1.8|SMC1|SMC1L1|SMC1alpha|SMCB
Cytomap

6p22.1

Xp11.22

Type of geneprotein-codingprotein-coding
Descriptiontripartite motif-containing protein 26RING finger protein 95acid finger proteinwidely expressed acid zinc finger proteinzinc finger protein 173structural maintenance of chromosomes protein 1ASMC protein 1ASMC-1-alphaSMC1 (structural maintenance of chromosomes 1, yeast)-like 1segregation of mitotic chromosomes 1
Modification date2018051920180522
UniProtAcc

P02771

Q14683

Ensembl transtripts involved in fusion geneENST00000395792, ENST00000226359, 
ENST00000506820, 
ENST00000322213, 
ENST00000469129, ENST00000375340, 
Fusion gene scores* DoF score2 X 2 X 2=84 X 4 X 3=48
# samples 24
** MAII scorelog2(2/8*10)=1.32192809488736log2(4/48*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: AFP [Title/Abstract] AND SMC1A [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
HgeneAFP

GO:0045087

innate immune response

18248090

HgeneAFP

GO:0046597

negative regulation of viral entry into host cell

18248090

HgeneAFP

GO:0051091

positive regulation of DNA binding transcription factor activity

23077300

HgeneAFP

GO:1902187

negative regulation of viral release from host cell

18248090

TgeneSMC1A

GO:0072423

response to DNA damage checkpoint signaling

11877377


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
TCGALDLIHCTCGA-DD-A73F-01AAFPchr4

74313259

+SMC1AchrX

53449595

-
* 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
5CDS-5UTRENST00000395792ENST00000322213AFPchr4

74313259

+SMC1AchrX

53449595

-
5CDS-intronENST00000395792ENST00000469129AFPchr4

74313259

+SMC1AchrX

53449595

-
5CDS-5UTRENST00000395792ENST00000375340AFPchr4

74313259

+SMC1AchrX

53449595

-
5CDS-5UTRENST00000226359ENST00000322213AFPchr4

74313259

+SMC1AchrX

53449595

-
5CDS-intronENST00000226359ENST00000469129AFPchr4

74313259

+SMC1AchrX

53449595

-
5CDS-5UTRENST00000226359ENST00000375340AFPchr4

74313259

+SMC1AchrX

53449595

-
intron-5UTRENST00000506820ENST00000322213AFPchr4

74313259

+SMC1AchrX

53449595

-
intron-intronENST00000506820ENST00000469129AFPchr4

74313259

+SMC1AchrX

53449595

-
intron-5UTRENST00000506820ENST00000375340AFPchr4

74313259

+SMC1AchrX

53449595

-

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FusionProtFeatures for AFP_SMC1A


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

P02771

SMC1A

Q14683

Binds copper, nickel, and fatty acids as well as, andbilirubin less well than, serum albumin. Only a small percentage(less than 2%) of the human AFP shows estrogen-binding properties. Involved in chromosome cohesion during cell cycle and inDNA repair. Central component of cohesin complex. The cohesincomplex is required for the cohesion of sister chromatids afterDNA replication. The cohesin complex apparently forms a largeproteinaceous ring within which sister chromatids can be trapped.At anaphase, the complex is cleaved and dissociates fromchromatin, allowing sister chromatids to segregate. The cohesincomplex may also play a role in spindle pole assembly duringmitosis. Involved in DNA repair via its interaction with BRCA1 andits related phosphorylation by ATM, or via its phosphorylation byATR. Works as a downstream effector both in the ATM/NBS1 branchand in the ATR/MSH2 branch of S-phase checkpoint.{ECO:0000269|PubMed:11877377}.

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 AFP_SMC1A


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.

* Fusion transcript sequences (only coding sequence (CDS) region).

* Fusion transcript sequences (Full-length transcript).

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FusionGenePPI for AFP_SMC1A


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
AFPSGSM2, CCR5, STAMBP, XIAP, PSMB7, GNB1, EHD4, MED27, AP4S1, PHB2, PIDD1SMC1ASTYXL1, CASP4, CDK4, ATM, SMC3, MSH6, CHTF18, SYCP3, SMARCA5, RAD21, NUMA1, STAG1, STAG3, RAE1, SMC1A, USP13, USP32, MLH1, ATRX, AIRE, ATG2A, ATG4C, BECN1, CAMKK2, PRKAA2, MGMT, SRRM1, RPGR, ATR, PHF1, CTCF, PAXIP1, THRA, THRB, KDM1B, EHMT2, SSU72, STAG2, PDS5A, PDS5B, WFDC5, BRCA1, HDAC5, WAPAL, BARD1, SMARCAD1, POLR2A, NIPBL, CDK8, CEBPA, MDC1, CUL3, CDK2, NSMCE2, FBXO6, MCM7, SF3B3, SMC2, RBM14, ACIN1, NOTCH1, METTL21B, MCM6, RFC1, POLA1, HDAC8, HDAC11, CDK20, ANKRD28, ARMCX3, KIF13A, RPA3, RPA2, RPA1, STAU1, CUL7, OBSL1, CCDC8, EED, RNF2, EGFR, SIRT6, ABCE1, ESR1, CDCA5, SDF4, PSMC2, NDC80, PLK1, POLE, SF3A2, SMC4, NTRK1, SCARNA22, HIST1H3E, BPTF, GANC, PEX1, HLTF, YWHAZ, SNX3, MRPL50, AKR7A2, SAP30, KCTD2, OSBPL3, PRPF19, KIAA1191, MTUS1, HAUS3, GCC1, NUF2, MGME1, LSM14B, DDI1, IRF3, TEAD2, FOXB1, FOXG1, FOXJ2, EP300, BRD4, FOXL1, FOXQ1, NF2, USP37, SNW1, CDC5L, RNF126, DERL1, USP15, SPAG9, MCM2, MCM4, EPS15L1, IVNS1ABP, GTF3C4, HSF1, NCL, MTF1


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 AFP_SMC1A


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 AFP_SMC1A


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneAFPC2239176Liver carcinoma3CTD_human
HgeneAFPC0023893Liver Cirrhosis, Experimental1CTD_human
HgeneAFPC0023895Liver diseases1CTD_human
HgeneAFPC0023904Liver Neoplasms, Experimental1CTD_human
HgeneAFPC0024668Mammary Neoplasms, Experimental1CTD_human
HgeneAFPC0038356Stomach Neoplasms1CTD_human
HgeneAFPC1458155Mammary Neoplasms1CTD_human
TgeneSMC1AC1802395Congenital muscular hypertrophy-cerebral syndrome5UNIPROT
TgeneSMC1AC0005695Bladder Neoplasm1CTD_human
TgeneSMC1AC0010606Adenoid Cystic Carcinoma1CTD_human
TgeneSMC1AC0023470Myeloid Leukemia1CTD_human