MPEP § 2412.05(c) — Representation and Inclusion of Variants (Annotated Rules)
§2412.05(c) Representation and Inclusion of Variants
This page consolidates and annotates all enforceable requirements under MPEP § 2412.05(c), including statutory authority, regulatory rules, examiner guidance, and practice notes. It is provided as guidance, with links to the ground truth sources. This is information only, it is not legal advice.
Representation and Inclusion of Variants
This section addresses Representation and Inclusion of Variants. Primary authority: 37 CFR 1.831(b) and 37 CFR 1.831(a). Contains: 2 requirements, 1 guidance statement, 1 permission, and 2 other statements.
Key Rules
Sequence Listing Format
[Editor Note: This section is applicable to all applications with a filing date, or, for national phase applications, an international filing date, on or after July 1, 2022, having disclosure of one or more nucleotide and/or amino acid sequences as defined in 37 CFR 1.831(b). Formatting representations of XML (eXtensible Markup Language) elements in this section appear different than shown in Standard ST.26, which may be accessed at: www.wipo.int /export/sites/www/standards/en/pdf/03-26-01.pdf.]
A primary sequence and any variant of that sequence, each disclosed by enumeration of its residues and meeting the definition in 37 CFR 1.831(a) and 1.831(b), must each be included in the “Sequence Listing XML” and assigned its own sequence identifier. Where a variant sequence is disclosed as a single sequence with enumerated alternative residues at one or more positions, it must be included in the “Sequence Listing XML” and should be represented by a single sequence, wherein the enumerated alternative residues are represented by the most restrictive ambiguity symbol. Any variant sequence, disclosed only by reference to deletion(s), insertion(s), or substitution(s) in a primary sequence, should be included in the “Sequence Listing XML”. The table below indicates the proper use of feature keys and qualifiers for nucleic acid and amino acid sequence variants:
A primary sequence and any variant of that sequence, each disclosed by enumeration of its residues and meeting the definition in 37 CFR 1.831(a) and 1.831(b), must each be included in the “Sequence Listing XML” and assigned its own sequence identifier. Where a variant sequence is disclosed as a single sequence with enumerated alternative residues at one or more positions, it must be included in the “Sequence Listing XML” and should be represented by a single sequence, wherein the enumerated alternative residues are represented by the most restrictive ambiguity symbol. Any variant sequence, disclosed only by reference to deletion(s), insertion(s), or substitution(s) in a primary sequence, should be included in the “Sequence Listing XML”. The table below indicates the proper use of feature keys and qualifiers for nucleic acid and amino acid sequence variants:
For additional information about the representation of sequence variants in a “Sequence Listing XML,” see MPEP § 2413.01(g), subsection XI.
Sequence Listing Content
[Editor Note: This section is applicable to all applications with a filing date, or, for national phase applications, an international filing date, on or after July 1, 2022, having disclosure of one or more nucleotide and/or amino acid sequences as defined in 37 CFR 1.831(b). Formatting representations of XML (eXtensible Markup Language) elements in this section appear different than shown in Standard ST.26, which may be accessed at: www.wipo.int /export/sites/www/standards/en/pdf/03-26-01.pdf.]
A primary sequence and any variant of that sequence, each disclosed by enumeration of its residues and meeting the definition in 37 CFR 1.831(a) and 1.831(b), must each be included in the “Sequence Listing XML” and assigned its own sequence identifier. Where a variant sequence is disclosed as a single sequence with enumerated alternative residues at one or more positions, it must be included in the “Sequence Listing XML” and should be represented by a single sequence, wherein the enumerated alternative residues are represented by the most restrictive ambiguity symbol. Any variant sequence, disclosed only by reference to deletion(s), insertion(s), or substitution(s) in a primary sequence, should be included in the “Sequence Listing XML”. The table below indicates the proper use of feature keys and qualifiers for nucleic acid and amino acid sequence variants:
A primary sequence and any variant of that sequence, each disclosed by enumeration of its residues and meeting the definition in 37 CFR 1.831(a) and 1.831(b), must each be included in the “Sequence Listing XML” and assigned its own sequence identifier. Where a variant sequence is disclosed as a single sequence with enumerated alternative residues at one or more positions, it must be included in the “Sequence Listing XML” and should be represented by a single sequence, wherein the enumerated alternative residues are represented by the most restrictive ambiguity symbol. Any variant sequence, disclosed only by reference to deletion(s), insertion(s), or substitution(s) in a primary sequence, should be included in the “Sequence Listing XML”. The table below indicates the proper use of feature keys and qualifiers for nucleic acid and amino acid sequence variants:
Citations
| Primary topic | Citation |
|---|---|
| Sequence Listing Content Sequence Listing Format | 37 CFR § 1.831(a) |
| Sequence Listing Content Sequence Listing Format | 37 CFR § 1.831(b) |
| Sequence Listing Format | MPEP § 2413.01(g) |
Source Text from USPTO’s MPEP
This is an exact copy of the MPEP from the USPTO. It is here for your reference to see the section in context.
Official MPEP § 2412.05(c) — Representation and Inclusion of Variants
Source: USPTO2412.05(c) Representation and Inclusion of Variants [R-01.2024]
[Editor Note: This section is applicable to all applications with a filing date, or, for national phase applications, an international filing date, on or after July 1, 2022, having disclosure of one or more nucleotide and/or amino acid sequences as defined in 37 CFR 1.831(b). Formatting representations of XML (eXtensible Markup Language) elements in this section appear different than shown in Standard ST.26, which may be accessed at: www.wipo.int /export/sites/www/standards/en/pdf/03-26-01.pdf.]
A primary sequence and any variant of that sequence, each disclosed by enumeration of its residues and meeting the definition in 37 CFR 1.831(a) and 1.831(b), must each be included in the “Sequence Listing XML” and assigned its own sequence identifier. Where a variant sequence is disclosed as a single sequence with enumerated alternative residues at one or more positions, it must be included in the “Sequence Listing XML” and should be represented by a single sequence, wherein the enumerated alternative residues are represented by the most restrictive ambiguity symbol. Any variant sequence, disclosed only by reference to deletion(s), insertion(s), or substitution(s) in a primary sequence, should be included in the “Sequence Listing XML”. The table below indicates the proper use of feature keys and qualifiers for nucleic acid and amino acid sequence variants:
| Type of sequence | Feature Key | Qualifier | Use |
|---|---|---|---|
| Nucleic acid | variation | replace or note | Naturally occurring mutations and polymorphisms, e.g., alleles, RFLPs. |
| Nucleic acid | misc_difference | replace or note | Variability introduced artificially, e.g., by genetic manipulation or by chemical synthesis. |
| Amino acid | VAR_SEQ | note | Variant produced by alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting. |
| Amino acid | VARIANT | note | Any type of variant for which VAR_SEQ is not applicable. |
Reproduced from paragraph 96 of WIPO Standard ST.26.
For additional information about feature keys and qualifiers, see MPEP § 2413.01(g), subsections II, III and V.
For additional information about the representation of sequence variants in a “Sequence Listing XML,” see MPEP § 2413.01(g), subsection XI.