If you use the ID, name and description parts, including the last comma, as the key to a hash entry and make the value an anonymous array onto which you push the application then you can print the key and then the joined elements quite simply.

use strict;
use warnings;

open my $inFH, q{<}, \ <<'EOD' or die qq{open: << HEREDOC: $!\n};
1,XYZ,desc,PDF
2,YGH,desc,KMN
1,XYZ,desc,QFZ
EOD

my %ids;
while ( <$inFH> )
{
    chomp;
    my ( $key, $value ) = m{^(.*,)(.*)$};
    push @{ $ids{ $key } }, $value;
}

print qq{$_@{ [ join q{,}, @{ $ids{ $_ } } ] }\n}
   for keys %ids;

close $inFH or die qq{close: << HEREDOC: $!\n};
[download]

The results.

1,XYZ,desc,PDF,QFZ
2,YGH,desc,KMN
[download]

Note that hashes are not ordered so if you want to impose a particular order in your output file you will need to sort the keys in some fashion. This exercise is left to the reader.

I hope this is useful.

Cheers,

JohnGG

Update: Corrected typo, s/nor/not/