Recommendations for the description of protein sequence variants (v2.0)

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)

Protein designations describe a sequence variant at amino acid level. Protein level variants will rarely be experimentally determined, i.e. using amino acid sequencing. In some cases indirect evidence might come from from sizing (Western blot analysis) or localisation (immuno-histochemical staining). In most cases protein descriptions will be deduced, predicted from the changes detected on DNA and/or RNA level.

Sequence changes at protein level are described like those at the DNA level with the following modifications / additions;

• a "p." is used to indicate description at protein level
• amino acids are described as "Trp26" (i.e. with Capital first letter, not as "trp26" or "Trp²⁶")
  • the three letter amino acid code is preferred to describe the amino acids (see Discussion)
  • "Ter" (3-letter code) or "*" (one-letter code) is used to designate a translation termination codon (see Important changes)
• 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 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, ...)
• 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)
• to indicate that the description at protein level is without any experimental proof it is recommended that, when RNA nor protein has been analysed, the description is given between brackets (e.g. p.(Arg22Ser), see Discussion 2012-10-12)
• protein variants
  • substitution variants are described using the format p.Trp26Cys and do not use the ">"-character (indicating "changes to") used on DNA- and RNA level
    • initiating methionine (Met1);  p.0,  p.Met1?,  p.Met1_Lys45del,  p.Met1ValextMet-12
    • nonsense;  p.Trp26*
    • no-stop change (stop codon);  p.*110Glnext*17
  • deletion variants are described using "del" after an indication of the first and last amino acid(s) deleted separated by a "_" (underscore);  p.Lys2del, p.Cys28_Met30del
  • duplication variants are described using "dup" after an indication of the first and last amino acid(s) duplicated separated by a "_" (underscore);  p.Gly4dup, p.His7_Gln8dup
  • inserstion variants are described using "ins" after an indication of the amino acids flanking the insertion site, separated by a "_" (underscore) and followed by a description of the amino acid(s) inserted;  p.Lys2_Met3insGln, p.Ala24_Thr25insGlnSerLys, p.Trp182_Gln183ins17
    NOTE: duplicating insertions should be described as duplications (see Discussion), not as insertion
  • variability of short sequence repeats are described as;  p.Gln6(3_6)
  • insertion-deletion variants (indels) are described using "delins" as a deletion followed by an insertion after an indication of the amino acid(s) flanking the site of the insertion/deletion separated by a "_" (underscore);  p.Cys28delinsTrpVal, p.Cys28_Met29delinsTrp
  • frame shift variants are described using "fs" after the first amino acid affected by the change. The description does not include the deletion at protein level from the site of the frame shift to the natural end of the protein (stop codon), so p.Arg97Profs*23 and not p.Arg97_Gln2309delProfs*23)
    • short ("fs");  p.Arg97fs
    • long ("fs*#");  p.Arg97Glyfs*16
      NOTE: the shifted reading frame includes the new amino acid (Gly) and is open for 15 amino acids
      NOTE: 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);  p.Glu5Valfs*5 and not something like p.Glu5Valins2fs*3
  • alleles are described using square brackets ("[ ]")
• for all descriptions the most 3' position possible is arbitrarily assigned to have been changed
• general descriptions
  • 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
    • p.=      - protein has not been analysed, RNA was, 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;
    • p0       - no protein can be detected (experimental data should be available)
    • p.0?    - probably no protein is produced 

Silent changes

Description of so called "silent" changes in the format p.(Leu54Leu) (or p.(L54L)) should not be used (correct is p.(=)); descriptions should be given at DNA level (see Discussion).

Substitutions

Substitutions have the format p.Trp26Cys and do not use the ">"-character (indicating "changes to") used on DNA- and RNA level.

• missense changes
  p.Trp26Cys denotes that amino acid Tryptophan-26 (Trp, W) is changed to a Cysteine (Cys)
• nonsense changes
  p.(Trp26*) indicates RNA nor protein was analysed but amino acid Tryptophan-26 (Trp, W) is predicted to change to a stop codon (*) (alternatively p.(W26*) or p.(Trp26Ter))
• initiating methionine changes (Met1)  (see Discussion,  see Examples)
  • p.0  -  no protein is produced (experimental data should be available)
  • 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
  • p.Met1_Lys45del  -  a new translation initiation site is activated (at Met46)
• date 2012-08-31 new translation initiation site  (see Discussion)
  • p.Met1ext-5  -  a variant in the 5' UTR activates a new upstream translation initiation site starting with amino acid Met-5 (Methionine -5)
  • p.Met1Valext-12  -  amino acid Met-1 is changed to Val activating an upstream translation initiation site at position -12 (Methionine-12)
    NOTE: recently modified from p.Met1ValextMet-12  (see Discussion)
• no-stop change  (substitution in stop codon)
  "ext*#" is used to indicate the extension of a protein sequence until a new stop codon is reached at "#" amino acids downstream as a consequence of a variant changing the natural stop codon into an amino acid.
  date 2012-11-01 When no stop codon is predicted this is indicated by "ext*?". 
  • p.*110Glnext*17 (alternatively p.*110Qext*17) describes a variant in the stop codon (*) at position 110, changing it to a codon for Glutamine (Gln, Q) and adding a tail of 17 new amino acids (incl. Gln110) to the protein's C-terminus after which a new stop codon (*17) is reached ('codon *127').
  • date 2012-11-01 p.*327Argext*? (alternatively p.*327Rext*?) describes a variant in the stop codon (*) at position 327, changing it to a codon for Arginine (Arg, R) and adding a tail of new amino acids of unknown length since the shifted frame does not contain a new stop codon (see FAQ).

Deletions

Deletions are described using "del" after an indication of the first and last amino acid(s) deleted separated by a "_" (underscore).

• 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 RNA nor protein was analysed but the predicted change is a deletion of three amino acids, from Cysteine-28 to Methionine-30

NOTE: for all descriptions the most 3' position possible is arbitrarily assigned to have been changed

Duplications

Duplications are described using "dup" after an indication of the first and last amino acid(s) duplicated separated by a "_" (underscore).

• 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)

NOTE: for all descriptions the most 3' position possible is arbitrarily assigned to have been changed

Insertions

Insertions are described using "ins" after an indication of the amino acids flanking the insertion site, separated by a "_" (underscore) and followed by a description of the amino acid(s) inserted. Duplicating insertions should be described as duplications (see Discussion), not as insertion. Since for large insertions the amino acids can be derived from the DNA and/or RNA descriptions they need not to be described exactly but the total number may be given (like "ins17").

• 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
• p.Trp182_Gln183ins17 describes a variant that inserts 17 amino acids between amino acids Trp182 and Gln183
  NOTE: it must be possible to deduce the 17 inserted amino acids for the description at DNA or RNA level

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 using "delins" as a deletion followed by an insertion after an indication of the amino acid(s) flanking the site of the insertion/deletion separated by a "_" (underscore, see Discussion).

• p.(Cys28_Lys29delinsTrp) indicates RNA nor protein was analysed but the predicted change is 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 variants are described using "fs" after the first amino acid affected by the change. Descriptions either use a short ("fs") or long ("fs*#") 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). 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).
NOTE: typing error in den "Dunnen & Antonarakis (2000)". The suggestion to use ">" to indicate "delins" in frame shift descriptions has been retracted.

• short description  -  uses "fs" only, e.g. p.Arg97fs
• long description  -  uses "fs*#" (see Discussion)
  • includes the change occurring at the site of the frame shift, e.g. p.Arg97Gly
  • "fs*#" indicates at which codon position the new reading frame ends in a stop (*). 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 (fs*#), e.g. p.Arg97Glyfs*16
    NOTE: the shifted reading frame is thus open for '#-1' amino acids
• Examples;
  • p.Arg97Profs*23 (not p.Arg97_Thr109delinsProfs*23; short p.Arg97fs) denotes a frame shifting change with Arginine-97 as the first affected amino acid, replacing it for 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.Glu5Valfs*5 describes a frame shifting insertion (do not use p.Glu5Valins2fs*3)
  • p.(Tyr4*) indicates RNA nor protein was analysed but the predicted consequence of the change c.12delC in the sequence ATG-GAT-GCA-TAC-GTG-ACG to ATG-GAT-GCA-TA.-G TG-A CG is a Tyr to translation termination codon.
  • p.Asp2Metfs*4 (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.Glu5Valfs*5 (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.
  • date 2012-11-01 p.Ile327Argfs*? (alternatively p.Ile327fs) describes the consequences of a frame shifting change (e.g. a 1-nucleotide insertion) with Isoleucine-327 as the first affected amino acid, replacing it for an Arginine and creating a new reading frame which does not encounter a new stop codon (see FAQ).

NOTE: the changes observed should be described on protein level and not try to incorporate any knowledge regarding the change at DNA-level (see Recommendation). Thus, p.His150Hisfs*10 is not correct, but p.Gln151Thrfs*9 is.

More changes in one individual

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

• Changes in different alleles (e.g. in recessive diseases) are described as "[change allele 1];[change allele 2]" (see Discussion).
  • p.[(Ala25Thr)];[(Ala25Thr)] indictes RNA nor protein was analysed but the predicted change is amino acid Alanine-25 to Threonine on both chromosomes (homozygous).
  • 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)
• Two variations in one allele
  • deriving from two independent changes at DNA level are described as "[first change;second change]" (see Discussion). 
    • p.[(Ala25Thr; Gly28Val)] indicates two predcited changes in one allele (RNA nor protein was analysed); 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.[Asn26His, Ala25_Gly29del] denotes two protein changes deriving from a change in one allele at DNA level (c.76A>C) resulting in two transcripts (r.[76a>c, 73_88del] ); amino acid Asparagine-25 to Histidine and a deletion of amino acids Asparagine-25 to Glycine-29
• Two sequence changes with alleles unknown are described as "[change 1(;)change 2]" (see Disucssion).
  • p.[Ala25Thr(;)Gly794Val] denotes that two changes were identified in one individual (amino acid Alanine-25 to Threonine and Glycine-794 to Valine), but it is not known whether these changes are in the same allele or in different alleles
• Mosaicism is described using "/"
  • p.[=/Arg83Ser] describes a mosaic organism or somatic tissue where the allele in some cells contain the normal sequence (Arg83 described as '='), while other cells contain a Ser at this position
• Chimerism is described using "//"
  • p.[=//Arg83Ser] describes a chimeric organism where the allele in some cells contain the normal sequence (Arg83 described as '='), while other cells contain a Ser at this position

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