Use case
Our database is combination with gene and clinical information, how to use our database about 3 user cases below.
  1. Search by amino acid change in gene
  2. Search by position in chromosome
  3. Search by disease are on our database
Search by amino acid change in gene
  1. Enter the gene name at search box and click [Search] icon.
    [Example] BRAF
  2. Search results are shown as below. Result page is consists of 7 tabs. [SNV/INDEL], [CNV] and [FUSION/SV] tab are shown about variants.


    Frequency is minor allele frequency associated with Japanese. (HGVD, ToMMo, ExAC_EAS).


    Prediction use the computational damaging prediction data(dbNSFP).
    Each prediction algorithms, show damage color or blank(no data).

    Prediction algorithms

    LRT(EC)、SIFT(EC)、FATHMM(EC)、MetaLR(ES)、MetaSVM(ES)、PROVEAN(AL)、GERP++、Realiability_index
    fitCons、PhyloP 100(NC)、PhyloP 20(NC)、GenoCanyon、FATHMM-MKL、Eigen-PC、MutationAssessor(EC)、MutationTaster2(PS)

  3. The first displayed varinats is MGeND data only. Select [All data] in [Display target variant] if you want to display all variants.
  4. Input keyword in filter box if you want filter on the search results. Only entries which match the input keyword [Example V600E] are shown. Click position entry if you want to show the detail variant information.
  5. Information page about BRAF V600E is shown.
Search by position in chromosome
  1. Click [Advanced] button in top page.
  2. Advanced search page is shown. Input the chromosome position in search box and click [Search] button.
    [Example] chr7:140453136-140453137
  3. Search result is shown.
Search by disease are on our database
  1. Select the disease area name in menu.


  2. Disease area page is shown. Disease page is the list of gene and diseases which find in the disease are. Click gene or disease if you want to show the detail (This image is the page of demo data).
Search result
Search results page is consists of below tabs.(For MGeND data, the background color of the header is blue.)
  1. SNV/INDEL
    Column Summary
    Variant name Show variant name.
    AA change Show Entrez Gene symbol and AA change.
    CDS Show RefSeq mRNA accession (If thers is no accession, show Ensembl transcript id) and nucleotide change.
    Japanese Frequency Show color of frequency (HGVD, ToMMo, ExAC(EAS)).
    Sample number Show sample number of MGeND(total numerator).
    Origin Show allele origin of MGeND.
    MGeND annotation Show clinical significance and rank star of MGeND.
    ClinVar entry Show entry number of ClinVar.
    ClinVar origin Show allele origin of ClinVar.
    ClinVar annotation Show clinical significance and rank star of ClinVar.
    CIViC evidence Show evidence number of CIViC.
    DisGeNET entry Show entry number of DisGeNET.
    Cosmic occurrence Show Cosmic occurrence.
    SnpEff impact Show variant impact and sequence ontology by SnpEff.
    dbNSFP prediction Show color of prediction damage by dbNSFP.
    It compiles prediction scores from prediction algorithms (LRT(EC), SIFT(EC), FATHMM(EC), MetaLR(ES), MetaSVM(ES), PROVEAN(AL), GERP++, Realiability_index, fitCons, PhyloP 100(NC), PhyloP 20(NC), GenoCanyon, FATHMM-MKL, Eigen-PC, MutationAssessor(EC), MutationTaster2(PS)).
    Search rank Show relevance score with search word.
  2. CNV
    Column Summary
    Name Show variant name.
    Sample number Show sample number of MGeND(total numerator).
    Origin Show allele origin of MGeND.
    MGeND annotation Show clinical significance and rank star of MGeND.
    Type Show variant type.
    Size Show variant size(stop -start + 1).
    Chromosome Show chromosome.
    Start Show start position.
    Stop Show stop position.
    Ref Show reference allele.
    Alt Show alternate allele.
    ClinVar Show clinical significance and rank star of ClinVar.
    Search rank Show relevance score with search word.
  3. FUSION/SV
    Column Summary
    Name Show variant name.
    Sample number Show sample number of MGeND(total numerator).
    Origin Show allele origin of MGeND.
    MGeND annotation Show clinical significance and rank star of MGeND.
    Type Show variant type.
    Gene symbol Show Entrez Gene symbol.
    Chromosome Show chromosome.
    Genomic start Show start position.
    Genomic stop Show stop position.
    Strand Show strand.
    Ref Show reference allele.
    Alt Show alternate allele.
    ClinVar Show clinical significance and rank star of ClinVar.
    Search rank Show relevance score with search word.
  4. CLINICAL TRIAL
    Column Summary
    NCT ID Show unique identification code given to each clinical study registered on ClinicalTrials.gov.
    Status Show the recruitment status for the clinical study as a whole, based upon the status of the individual sites.
    Phase Show clinical trial of a drug product (including a biological product), the numerical phase of such clinical trial
    Summary Show a short title of the clinical study written in language intended for the lay public.
    Start date Show the date the study started in a date-type format so that it can be used to find studies before/after/inclusive of a date or dates.
    Completion date Show the final participant was examined or received an intervention for purposes of final collection of data for the primary and secondary outcome measures and adverse events.