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#!/usr/bin/env perl

...
    my $alt = join '|', @list;
    return (\@list, qr{($alt)});
}

$ cat pm_1192233_genes.txt
ACMSD
...
CRYM 3
ARIB1B 3
ZZZZ 3

$ pm_1192233_multi_file_output.pl pm_1192233_anot_*
$

$ cat pm_1192233_out_ACMSD
ACMSD 1
...
GENE_NOT_ANOTATED
ALSO_ABSENT
--- END MISSING LIST ---