use Sort::Key::Multi qw(u3_keysort); # u3 stands for 3 unsigned integer keys

my $ix = 0;
my %map_10th = map { $_ => $ix++ } qw(GENE UTR ...);

my @data = ...;
my @sorted = u3_keysort {
               my @key = split /\s+/;
               ($key[0], $key[1], $map_10th{$key[9]})
             } @data;