If you structure your data a little differently, it will be easier to extract what you need:

use strict;
use warnings;
use List::Util qw(max min);

my %gene_hash;
while (<DATA>) {
    chomp;
    my ($chr, $start, $end, $gene, $ex) = split /\t/;
    push @{ $gene_hash{$chr}{$gene}{start} }, $start;
    push @{ $gene_hash{$chr}{$gene}{end  } }, $end;
    push @{ $gene_hash{$chr}{$gene}{ex   } }, $ex;
}

for my $chr (keys %gene_hash) {
    for my $gene (keys %{ $gene_hash{$chr} }) {
        my $Low     = min( @ { $gene_hash{$chr}{$gene}{start} } );
        my $High    = max( @ { $gene_hash{$chr}{$gene}{end  } } );
        my $High_ex = max( @ { $gene_hash{$chr}{$gene}{ex   } } );
        print "$chr $Low $High $gene $High_ex\n";
    }
}

__DATA__
chrX    2680092    2744539    XG    1
chrX    2680090    2744529    XG    2
chrX    2680080    2744519    XG    3
chrX    2680070    2744509    XG    4
chrX    2680070    2744509    DT    1
chrX    2680090    2744519    DT    2
[download]

prints out:

chrX 2680070 2744539 XG 4
chrX 2680070 2744519 DT 2
[download]