Protein Recommendations

Deletion Variant


Definitions

Deletion
a sequence change where, compared to a reference sequence, one or more amino acids are not present (deleted).

Description

Format: “prefix”“amino_acid(s)+position(s)_deleted”“del”, e.g. p.Cys76_Glu79del

“prefix” = reference sequence used = p.
“amino_acid(s)+position(s)_deleted” = amino acid with position or range (first amino acid with position to last amino acids with position) deleted = Cys76_Glu79
“del” = type of change is a deletion = del


Note

  • prefix reference sequence accepted is “p.” (protein).
  • predicted consequences, i.e. without experimental evidence (no RNA or protein analysed), should be given in parentheses, e.g. p.(Arg727_Ser783del).
  • the “amino_acids+positions_deleted” should contain two different positions, e.g. Cys76_Glu79, not Cys76_Cys76.
  • the “positions_deleted” should be listed from 5’ to 3’, e.g. Cys76_Glu79, not Glu79_Cys76.
  • for all descriptions the most C-terminal position possible of the reference sequence is arbitrarily assigned to have been changed (3’rule).
    • the 3’rule also applies for changes in single amino acid stretches and tandem repeats.
  • variants should be described on the protein level and not incorporate knowledge regarding the change at the DNA level.
  • in theory, a nonsense variant can be considered as a deletion removing the C-terminal end of the protein (e.g. p.Trp26_Arg1623del). However, in HGVS nomenclature, nonsense variants are described as an amino acid substitution (p.Trp26Ter or p.Trp26* see Substitution) replacing the first amino acid affected by a translation termination (stop) codon.

Examples

  • p.Ala3del (one amino acid)
    a deletion of amino acid Ala3 in the sequence MetGlyAlaArgSerSerHis to MetGly_ArgSerSerHis
  • p.(Ala3del)
    the predicted consequence at the protein level is a deletion of amino acid Ala3 in the sequence MetGlyAlaArgSerSerHis to MetGly_ArgSerSerHis
  • p.Ala3_Ser5del (several amino acids)
    a deletion of amino acids Ala3 to Ser5 in the sequence MetGlyAlaArgSerSerHis to MetGly___SerHis
  • p.Ser6del
    a deletion of amino acid Ser in the sequence MetGlyAlaArgSerSerHis to MetGlyAlaArgSer_His
    NOTE:_ for deletions in single amino acid stretches or tandem repeats, the most C-terminal residue is arbitrarily assigned to have been deleted
  • p.Gly2_Met46del
    a deletion of amino acids Gly2 to Met46 as a consequence of a variant silencing translation initiation ate Met1 but activating a new downstream translation initiation site (at Met46)
    NOTE: the 3’ rule has been applied.
  • p.Trp26Ter (p.Trp26*)
    amino acid Trp26 is changed to a stop codon (Ter, *)
    NOTE: this change is not described as a deletion of the C-terminal end of the protein (i.e. p.Trp26_Arg1623del)

Q&A

Can I use p.Arg45del6 to describe a 6 amino acid deletion?

No, a deletion of more than one residue should mention the first and last residue deleted, separated using the range symbol ("_", underscore), e.g. p.Arg45_Gly50del and not p.Arg45del6.

Is the description of a deletion of exon 17 as p.EX17del still allowed?

A description like p.EX17del has never been allowed. Descriptions should be specific and indicate the amino acids affected by the change.

In literature I often see the description "deltaF508" for a variant in the CFTR gene in patients with Cystic Fibrosis. Is this according to HGVS nomenclature a correct description

No, the correct description of this variant at the protein level is p.Phe508del.

What do you mean with "variants should be described on the protein level and not incorporate knowledge regarding the change at the DNA-level"?

It means that protein variant descriptions should be derived from comparing the variant protein sequence with the reference protein sequence. Knowledge on the underlying change at the DNA level should not be used. E.g. when MetTrpSerSerSerHisAsp.. changes to MetTrpSerSer_HisAsp.. this is described as p.Ser5del. The information that at the DNA level the change is ..ATGTGGTCCAGTTCCCACGAT.. to ..ATGTGGTCC_TCCCACGAT.., so the codon for Ser4 is deleted, is not used; the description p.Ser4del is not correct.