The code sample you provide doesn't match the sample data you provide and you don't show the expected output for the sample data so the following is rather a guess:

use strict;
use warnings;

my %clone_hash;

while (<DATA>) {
    chomp;
    next if ! length;
    
    my ($gene_symbol, $esc_qc) = split /\s+/;

    $clone_hash{$gene_symbol}{$esc_qc}++;
}

my $okGenes = 0;
my $singleOks = 0;

foreach my $key (sort keys %clone_hash) {
    my $gene = $clone_hash{$key};
    my $okPasses = grep {defined} @{{%$gene}}{qw(pass1 pass2 pass3)};
    my $badPasses = keys (%$gene) - $okPasses;
    
    if ($badPasses) {
        ++$singleOks if $okPasses == 1;
    } else {
        ++$okGenes;
    }
}

print "Ok genes:          $okGenes\n";
print "Single pass genes: $singleOks\n";

__DATA__
Eif2b2    fail
Eif2b2    pass5
Eif2b2    fail
Eif2b2    pass2
Eif2b2    fail
Eif2b2    pass4
Eif2b2    fail
49334    fail
49334    fail
49334    pass1
49334    fail
49334    pass4
Oxct1    pass4
Oxct1    fail
Oxct1    pass4
Oxct1    fail
[download]

Prints:

Ok genes:          0
Single pass genes: 2
[download]