#!/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;
}

##</code><code>##

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