Frequently Asked Questions

How are insertions and deletions, nonsense, frameshift, and non-coding variants displayed in Mastermind?

Mastermind uses shorthand identifiers to represent each type of variant in the protein space. The shorthands used by Mastermind are as follows:

• Insertions: “ins” — e.g. V600ins
• Deletions: “del” — e.g. V600del
• Indels: “delins” — e.g. V600delins
• Nonsense: “X” — e.g. V600X
• Frameshift: “fs” — e.g. V600fs
• Untranslated regions: “UTR” — e.g. 5’UTR or 3’UTR. Some genes also contain introns within the untranslated regions, so all of the following splice and intron categories below may be appended to the UTR categories for untranslated regions that contain introns. For example a splice donor “sd” variant that occurs in an intron inside the 5’UTR will appear as 5’UTRsd in Mastermind.
• Splice donor: “sd” — e.g. V168sd; these are variants affecting the 2-base region at the 5′ side of the intron. In the protein space, these are mapped to the nearest amino acid in the nearest coding neighbor at the 5′ side of the intron.
• Splice acceptor: “sa” — e.g. N581sa; these are variants affecting the 2-base region at the 3′ side of the intron. In the protein space, these are mapped to the nearest amino acid in the nearest coding neighbor at the 3′ side of the intron.
• Intronic: “int” — e.g. E46int; these are variants affecting any of the bases within the intron between the splice acceptor and splice donor sites. In the protein space, these are mapped to the nearest amino acid in the nearest coding neighbor.
• Intonic donor and acceptor sides: “intd” and “inta” — e.g. N581intd or N581inta; these are variants that occur in either the donor half or the acceptor half of the Intronic “int” variant region between the splice donor and splice acceptor sites. These are more specific sub-divisions of the “int” category, and so variants in either the “intd” or “inta” categories will appear in the “int” category as well.
• Splice regions: “srd” and “sra” — e.g. N581srd or N581sra; these are variants surrounding the splice sites, from 1 to 3 bases into the exon and from 3 to 8 bases into the intron. The intronic part of the splice regions overlap the intronic “int” classification as well, so splice region variants within the intron will also appear in the “int” and either the “intd” or “inta” categories as well.
• Upstream genetic variant: “ugv” — only ugv; these are variants affecting the region of 5,000 bases upstream of the 5′ side of the gene.
• Downstream genetic variant: “dgv” — only dgv; these are variants affecting the region of 5,000 bases downstream of the 3′ side of the gene.
• Extensions: “ext” — e.g. A55int; these are variants which span multiple exons within the gene.

The “Filter by” input in the “Variants” section of the Mastermind results page can be used to find such variants. For example, typing “ins” or “del” will filter the results for all insertions and deletions cited in that gene. Other shorthands can be used in the same way.