This one should work:
awk 'BEGIN{ OFS = "\t" }NR==1{ for ( i = 1; i <= NF; i++) if ( $i ~"Pval" ) a[i]; print $0}NR>1{for ( i in a ) if ( $i > 0.5 ) $i = "NA"; print $0 }' file
Output:
Rv_FC Rv_Pval Gc_FC Gc_Pval
2 0.001 3 NA
3 NA 1 0.0002
3 0.0001 2 NA
7
solved Filtering and replacing from multiple columns