It is not too late to insert <code> tags into your original post. You are able to update it any time.

As I understand you just want to output unique names of genes instead of raw rows. Than try this

#!/usr/bin/perl -lan
# Usage: thisscript.pl genes.txt

if ( $seen{ join ' ', sort @F }++ ) {
    $uniq{$F[0]}++;
    $uniq{$F[1]}++;
}
END {
    print for keys %uniq;
}
[download]

And this:

Linux version:
perl -lane '@u{@F}=() if $s{join "", sort @F}++ }{ print for keys %u' 
+genes.txt

Windows version:
perl -lane "@u{@F}=() if $s{join '', sort @F}++ }{ print for keys %u" 
+genes.txt
[download]

Where genes.txt is a file containing gene rows

Feel free to ask if you need explanations on the algorithm and it's implementation.