Recommendations for the description of protein sequence variants

Since references to WWW-sites are not yet acknowledged as citations, please mention den Dunnen JT and Antonarakis SE (2000). Hum.Mutat. 15:7-12 when referring to these pages.

Contents

• Recommendations
  • general recommendations
  • changes at protein level
    • general
    • silent changes
    • substitutions - no-stop change
    • deletions
    • duplications
    • insertions
    • variability of short sequence repeats
    • insertion-deletions  (indels)
    • frame shifts
    • more changes in one individual
  • changes at DNA level
  • changes at RNA level
• Explanations / examples
  • Quick Reference
  • changes at DNA level
  • changes at RNA level
  • changes at protein level
• Codons and encoded amino acids
  • genetic code
  • amino acid descriptions  (one and three letter code)

Protein level

(suggestions extending the published recommendations in italics)

Designations at protein level describe the consequence of a change, the origin lies at DNA-level, and they will be rarely experimentally verified. Sequence changes at protein level are described as those at the DNA level with the following modifications / additions;

• when changes at protein level are described it should be clear whether the changes were experimentally determined or only theoretically deduced
• a "p." is used to indicate description at protein level
• descriptions at protein level should describe the changes observed on protein level and not try to incorporate any knowledge regarding the change at DNA-level  (see FAQ)
  • the description of frame shifts does not include the deletion at protein level from the site of the frame shift to the natural C-terminal end (stop codon) of the protein (so p.Arg97ProfsX23 and not p.Arg97_Pro109delfsX23). Similarly, for frame shifting insertions the inserted amino acid residues are not described, only the total length of the new shifted frame is given (i.e. including the inserted amino acids), so p.Glu5ValfsX5 and not something like p.Glu5Valins2fsX3.
• amino acid numbering
  • the translation initiator Methionine is numbered as +1
  • the protein reference sequences should represent the primary translation product, not a processed mature protein, and thus include any signal peptide sequences (see FAQ)
  • amino acids originating from changes introducing upstream translation initiation are numbered like nucleotides (like ..., Gln-2, Thr-1)
  • amino acids originating from changes resulting in translation of intronic sequences are numbered like nucleotides (like Val4+1, Ser4+2, ..., Phe5-2, Gln5-1)
  • amino acids originating from no-stop changes causing translation downstream of the translation termination codon numbered like nucleotides (like Gln*1, Ser*2, ...)
• the three letter amino acid code is preferred to describe the amino acids (see Discussion)
  • amino acids are described as "Trp26" (i.e. with Capital first letter, not as "trp26" or "Trp²⁶")
  • "X" is used to designate a translation termination codon

Silent changes

Description of so called "silent" changes in the format p.Leu54Leu (or p.L54L) is not allowed; descriptions should be given at DNA level. The description at protein level is not informative and not unequivocal (there are five possibilities at DNA level which may underlie p.Leu54Leu). A correct description has the format c.162C>G (p.=), with "p.=" indicating that there is no effect on protein level expected (see Discussion).

Substitutions

Substitutions are designated by a ">"-character (indicating "changes to").

• missense changes
  p.Trp26Cys denotes that amino acid Tryptophan-26 (Trp, W) is changed to a Cysteine (Cys).
• initiating methionine (Met1)  (see Discussion)
  • p.Met1? denotes that amino acid Methionine-1 (translation initiation site) is changed and that it is unclear what the consequence of this change is. When experimental data show that no protein is made, the description p.0 can be used.
  • p.Met1ValextMet-12 denotes that the translation initiating Methionine is changed to a Valine, activating an upstream translation initiation site starting at position -12 (Methionine-12)
• nonsense changes
  p.Trp26X denotes that amino acid Tryptophan-26 (Trp, W) is changed to a stop codon (X).
• no-stop change  (substitution in stop codon)
  "extX#" is used to indicate the extension of a protein sequence when the stop codon changes to an amino acid with "X#" indicating the length of the extended reading frame
  NOTE: for counting the length of the extended reading frame includes the stop codon (X110) that changes to an amino acid.
  • p.X110GlnextX17 (alternatively p.X110QextX17) denotes a change in the stop codon (X) at position 110, changing it to a codon for Glutamine (Gln, Q) and adding a tail of 16 new amino acids to the protein's C-terminus after which a new stop codon (X17) is reached.
• unknown effect
  • p.?       - protein has not been analysed, an effect is expected but difficult to predict
  • p.(=)    - protein has not been analysed, but no change is expected
  • amount of protein
    changes which affect the promoter of a gene, the transcription initiation site (cap site), the translation initiation site, etc. may affect the amount of protein produced. Similarly, a deletion of the promoter / exon 1 region usually has the effect that no protein is produced (or that other promoters are activated).
    • p0       - no protein can be detected
    • p.0?    - probably no protein is produced 

Deletions

Deletions are designated by "del" after an indication of the first and last amino acid(s) deleted.

• p.Lys2del in the sequence MKMGHQQQCC denotes a deletion of amino acid Lysine-2 (Lys, K) to MMGHQQQCC
• p.Gln8del in the sequence MKMGHQQQCC denotes a Glutamine-8 (Gln, Q) deletion to MKMGHQQCC
• p.Cys28_Met30del denotes a deletion of three amino acids, from Cysteine-28 to Methionine-30
• if a non-frame shifting deletion creates a new amino acid at the deletion junction the change is described as a insertion/deletion, e.g. p.Cys28_Met29delinsTrp (see Discussion)

Duplications

Duplications are designated by "dup" after an indication of the first and last amino acid(s) duplicated.

• p.GLy4_Gln6dup in the sequence MKMGHQQQCC denotes a duplication of amino acids Glycine-4 (Gly, G) to Glutamine-6 (Gln, Q) (i.e. MKMGHQGHQQQCC)
• duplicating insertions in single amino acid stretches (or short tandem repeats) are described as a duplication, e.g. a duplicating HQ insertion in the HQ-tandem repeat sequence of MKMGHQHQCC to MKMGHQHQHQCC is described as p.His7_Gln8dup (not p.Gln8_Cys9insHisGln)

Insertions

Insertions are designated by "ins" after an indication of the amino acids flanking the insertion site, followed by a description of the amino acid(s) inserted. Duplicating insertions should be described as duplications (see Discussion), not as insertion. For large insertions the number of inserted amino acids should be mentioned, together with an accession.version number referring to a sequence database file containing the complete inserted sequence. 

• p.Lys2_Met3insGlnSerLys denotes that the sequence GlnSerLys (QSK) was inserted between amino acids Lysine-2 (Lys, K) and Methionine-3 (Met, M), changing MKMGHQQQCC to MKQSKMGHQQQCC
• if a non-frame shifting insertion creates a new amino acid at the insertion junction the change is described as an insertion/deletion, e.g. p.Cys28delinsTrpVal (see Discussion)

Variability of short sequence repeats

Variability of short sequence repeats are described as p.Gln6(3_6); the description indicates that a stretch of Glutamines (Gln, Q) is present, starting at amino acid position 6 (e.g. in MKMGHQQQCC), which is found with a variable length from 3 to 6 in the population.
NOTE: the underscore is used to indicate the range (3 to 6 times).

Insertion-deletions (indels)

Insertion/deletions (indels) are described as a deletion followed by an insertion after an indication of the amino acid(s) flanking the site of the insertion/deletion (see Discussion).

• p.Cys28_Lys29delinsTrp denotes a 3 bp deletion that affects the codons for Cysteine-28 and Lysine-29, substituting them for a codon for Tryptophan
• p.Cys28delinsTrpVal denotes a 3 bp insertion in the codon for Cysteine-28, generating codons for Tryptophan (Trp, W) and Valine (Val, V)

Frame shifts

Frame shifting mutations are designated by "fs" after the amino acid(s) affected by the change. Descriptions either use a short ("fs") or long ("fsX#") description. The description of frame shifts does not include the deletion at protein level from the site of the frame shift to the natural end of the protein (stop codon).
NOTE: typing error in den "Dunnen & Antonarakis (2000)". The suggestion to use ">" to indicate "delins" in frame shift descriptions has been retracted.
NOTE: also for frame shifts the changes observed should be described on protein level and not try to incorporate any knowledge regarding the change at DNA-level (see above). Thus, p.His150HisfsX10 is not correct, but p.Gln151ThrfsX9 is.

• short description  -  uses "fs" only, e.g. p.Arg97fs
• long description  -  uses "fsX#" (see Discussion)
  • includes the change occurring at the site of the frame shift, e.g. p.Arg97Gly
  • "X#" indicates at which codon position the new reading frame ends in a stop (X). The position of the stop in the new reading frame is calculated starting at the first changed amino acid that is created by the frame shift, and ending at the first stop codon (X#), e.g. p.Arg97GlyfsX16
    NOTE: the shifted reading frame is thus open for '#-1' amino acids
• Examples;
  • p.Arg97ProfsX23 (not p.Arg97_Pro109delfsX23; short p.Arg97fs) denotes a frame shifting change with Arginine-97 as the first affected amino acid, changing to a Proline and creating a new reading frame ending in a stop at position 23 (counting starts with the Proline as amino acid 1).
  • p.Leu30SerfsX3 (not p.Leu30_Cys42delinsSerfsX3; short p.Leu30fs) denotes a frame shifting change that deletes amino acids Leucine-30 to Cysteine-42, substituting these for a Serine at the deletion junction and creating a new reading frame ending in a stop at position 3 (counting starts with the Serine as amino acid 1). 
  • p.Tyr4X describes the consequence of the change c.12delC in the sequence ATG-GAT-GCA-TAC-GTG-ACG to ATG-GAT-GCA-TA.-G TG-A CG.
  • p.Asp2MetfsX4 (alternatively p.Asp2fs) describes the consequence of the change c.4delG in the sequence ATG-GAT-GCA-TAC-GTG-ACG to ATG- .AT-G CA-T AC-G TG-A CG.
  • p.Glu5ValfsX5 (alternatively p.Glu5fs) describes the consequence of the change c.6_13dup in the sequence ATG-GAT-GCA-TAC-GAG-ATG-AGG  to ATG-GAT-GCA-TAC-GT-G CA-T AC-G AG-A TG-A GG.
    NOTE: the inserted amino acids are not specified (see Recommendation)

More changes in one individual

Two or more changes in one individual are described by combining the changes, per allele (chromosome) between brackets ("[]").

• p.[Ala25Thr]+[Ala25Thr] denotes a homozygous change of amino acid Alanine-25 to Threonine.
• p.[Ala25Thr]+[?] denotes a change of amino acid Alanine-25 to Threonine in one allele and an unknown change in the other allele
  NOTE: "unknown change in the other allele" does not only mean that no DNA-change was detected in that other allele but includes cases where the consequence of a detected change is unclear or can not be predicted (e.g. the consequence of a change at the splice site)
• p.[Ala25Thr]+[=] denotes a change of amino acid Alanine-25 to Threonine in one allele and a normal sequence (indicated by "=") in the other allele (see FAQ)

• deriving from two independent changes at DNA level are described as "[first change;second change]" (see Discussion). 
  • p.[Ala25Thr;Gly28Val] denotes two changes in one allele; amino acid Alanine-25 to Threonine and Glycine-28 to Valine
• deriving from one change at DNA level that has more than one effect on RNA/protein level are described as "[first change, second change]" (see Discussion). 
  • p.[Ala5Thr, Ala5_Gly30delfsX] denotes two protein changes deriving from a change in one allele at DNA level (c.13G>A, see Figure) resulting in two transcripts (r.[13g>a, 13_88del]); amino acid Alanine-5 to Threonine and a deletion of amino acids Alanine-5 to Glycine-30 followed by a frame shift

• p.[Ala25Thr(+)Gly94Val] denotes that two changes were identified in one individual (amino acid Alanine-25 to Threonine and Glycine-94 to Valine), but it is not known whether these changes are in the same allele or in different alleles

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