use Data::Dumper;
local $\="\n";

$a = {
    gene => { id => 3, label => 'generrrous' }
};

print $a->{ gene, id}=1;
print $a->{ gene => id };
print Dumper $a;

__END__
1
1
$VAR1 = {
          'gene' => {
                      'label' => 'generrrous',
                      'id' => 3
                    },
          'gene‡˜id' => 1
        };