How To Locate 'Rsxxxx' Number For H1069Q Mutation On Atp7B Gene?

Question

[Inquisitor]

How can I search & locate the snp / rs number for H1069Q and G1267R snps on ATP7B gene?

Answer 1

[Pierre Lindenbaum]

here is the output of my tool backlocate

$ echo -e  "ATP7B\tH1069Q\nATP7B\tG1267R" | \
java -cp backlocate.jar:mysql-connector.jar  sandbox.BackLocate 
#User.Gene    AA1    petide.pos.1    AA2    knownGene.name    knownGene.strand    knownGene.AA    index0.in.rna    codon    base.in.rnachromosome    index0.in.genomic    exon
##Warning ref aminod acid for uc010tgt.1  [1069] is not the same (P/H)
ATP7B    H    1069    Q    uc010tgt.1    -    P    3204    CCC    C    chr13    52516533    Exon 14
ATP7B    H    1069    Q    uc010tgt.1    -    P    3205    CCC    C    chr13    52516532    Exon 14
ATP7B    H    1069    Q    uc010tgt.1    -    P    3206    CCC    C    chr13    52516531    Exon 14
##Warning ref aminod acid for uc010tgu.1  [1069] is not the same (E/H)
ATP7B    H    1069    Q    uc010tgu.1    -    E    3204    GAG    G    chr13    52516584    Exon 15
ATP7B    H    1069    Q    uc010tgu.1    -    E    3205    GAG    A    chr13    52516583    Exon 15
ATP7B    H    1069    Q    uc010tgu.1    -    E    3206    GAG    G    chr13    52516582    Exon 15
##uc001vfw.2
ATP7B    H    1069    Q    uc001vfw.2    -    H    3204    CAC    C    chr13    52518282    Exon 14
ATP7B    H    1069    Q    uc001vfw.2    -    H    3205    CAC    A    chr13    52518281    Exon 14
ATP7B    H    1069    Q    uc001vfw.2    -    H    3206    CAC    C    chr13    52518280    Exon 14
##Warning ref aminod acid for uc001vfy.2  [1069] is not the same (I/H)
ATP7B    H    1069    Q    uc001vfy.2    -    I    3204    ATC    A    chr13    52515234    Exon 17
ATP7B    H    1069    Q    uc001vfy.2    -    I    3205    ATC    T    chr13    52515233    Exon 17
ATP7B    H    1069    Q    uc001vfy.2    -    I    3206    ATC    C    chr13    52515232    Exon 17
#index out of range for :uc001vfv.2 petide length=738
#index out of range for :uc010tgw.1 petide length=529
#index out of range for :uc010adv.2 petide length=1036
#index out of range for :uc010tgs.1 petide length=677
##Warning ref aminod acid for uc010tgv.1  [1069] is not the same (L/H)
ATP7B    H    1069    Q    uc010tgv.1    -    L    3204    CTG    C    chr13    52515333    Exon 15
ATP7B    H    1069    Q    uc010tgv.1    -    L    3205    CTG    T    chr13    52515332    Exon 15
ATP7B    H    1069    Q    uc010tgv.1    -    L    3206    CTG    G    chr13    52515331    Exon 15
##Warning ref aminod acid for uc001vfx.2  [1069] is not the same (A/H)
ATP7B    H    1069    Q    uc001vfx.2    -    A    3204    GCC    G    chr13    52511688    Exon 14
ATP7B    H    1069    Q    uc001vfx.2    -    A    3205    GCC    C    chr13    52511687    Exon 14
ATP7B    H    1069    Q    uc001vfx.2    -    A    3206    GCC    C    chr13    52511686    Exon 14
##Warning ref aminod acid for uc010tgt.1  [1267] is not the same (N/G)
ATP7B    G    1267    R    uc010tgt.1    -    N    3798    AAC    A    chr13    52511438    Exon 18
ATP7B    G    1267    R    uc010tgt.1    -    N    3799    AAC    A    chr13    52511437    Exon 18
ATP7B    G    1267    R    uc010tgt.1    -    N    3800    AAC    C    chr13    52511436    Exon 18
##Warning ref aminod acid for uc010tgu.1  [1267] is not the same (K/G)
ATP7B    G    1267    R    uc010tgu.1    -    K    3798    AAG    A    chr13    52511489    Exon 19
ATP7B    G    1267    R    uc010tgu.1    -    K    3799    AAG    A    chr13    52511488    Exon 19
ATP7B    G    1267    R    uc010tgu.1    -    K    3800    AAG    G    chr13    52511487    Exon 19
##Warning ref aminod acid for uc001vfw.2  [1267] is not the same (D/G)
ATP7B    G    1267    R    uc001vfw.2    -    D    3798    GAT    G    chr13    52511715    Exon 18
ATP7B    G    1267    R    uc001vfw.2    -    D    3799    GAT    A    chr13    52511714    Exon 18
ATP7B    G    1267    R    uc001vfw.2    -    D    3800    GAT    T    chr13    52511713    Exon 18
##Warning ref aminod acid for uc001vfy.2  [1267] is not the same (K/G)
ATP7B    G    1267    R    uc001vfy.2    -    K    3798    AAG    A    chr13    52509157    Exon 22
ATP7B    G    1267    R    uc001vfy.2    -    K    3799    AAG    A    chr13    52509156    Exon 22
ATP7B    G    1267    R    uc001vfy.2    -    K    3800    AAG    G    chr13    52509155    Exon 22
#index out of range for :uc001vfv.2 petide length=738
#index out of range for :uc010tgw.1 petide length=529
#index out of range for :uc010adv.2 petide length=1036
#index out of range for :uc010tgs.1 petide length=677
##Warning ref aminod acid for uc010tgv.1  [1267] is not the same (P/G)
ATP7B    G    1267    R    uc010tgv.1    -    P    3798    CCC    C    chr13    52509819    Exon 19
ATP7B    G    1267    R    uc010tgv.1    -    P    3799    CCC    C    chr13    52509818    Exon 19
ATP7B    G    1267    R    uc010tgv.1    -    P    3800    CCC    C    chr13    52509817    Exon 19
#index out of range for :uc001vfx.2 petide length=1259

uc001vfw.2 is the only transcript for ATP7B having a correct AA at 1069. The rs## at this position are:

$ mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e 'select chrom,name,chromStart,chromEnd from hg19.snp137 where chrom="chr13" and chromStart in (52518282,52518281,52518280)'
+-------+-------------+------------+----------+
| chrom | name        | chromStart | chromEnd |
+-------+-------------+------------+----------+
| chr13 | rs76151636  |   52518280 | 52518281 |
| chr13 | rs201738147 |   52518280 | 52518281 |
| chr13 | rs201738147 |   52518281 | 52518282 |
+-------+-------------+------------+----------+