You could create a Hash-of-Arrays data structure. The hash keys could be a concatenation of the 1st 3 columns, and the hash values could be an array of all the last column values:

use strict;
use warnings;

my %data;
while (<DATA>) {
    my @cols = split;
    my $col3 = pop @cols;
    my $key = "@cols";
    push @{ $data{$key} }, $col3;
}

for (keys %data) {
    print "$_ ", join(',', @{ $data{$_} }), "\n";
}

__DATA__
chr1 12345 34567 gene1 
chr1 12345 34567 gene2
[download]

Output:

chr1 12345 34567 gene1,gene2
[download]