We may observe 74 pLoF variants in the database across all transcripts and variant types in this gene, but the constraint table only displays pLoF variants that meet the following criteria:
- single nucleotide variants
- in the MANE Select transcript
- with MAF < 0.1%
- that are considered high confidence by LOFTEE
- in the exome sequenced samples
For this particular gene, if you go to the page for the MANE select transcript (gnomAD), you will see 66 pLoF variants listed. Of those, only 5 are considered “high confidence” (as noted by the lack of the LC pLoF flag) and only two are single nucleotide variants.
One faster way to find this is to uncheck “Genomes” and “indels” and then sort by the “Flags” column:
