A custom AI reviewer for variant and gene nomenclature

PerfectPaper’s nomenclature agent reads a genomics manuscript for variant and gene naming errors: variant strings that do not follow HGVS syntax, transcript references given without a version, protein and coding descriptions that disagree, and gene symbols that have been superseded or that collide with an alias. Copy the brief below into a custom agent slot.

This is the narrowest agent in the set and the fastest to act on. Nomenclature errors are unambiguous, they propagate into databases, and they are trivially fixable once found.

When to use this agent

• Your manuscript reports specific sequence variants
• Variants are described in text, a table and a figure, and were typed more than once
• The paper has co-authors who used different conventions
• You are reporting clinical or germline variants that will be curated downstream
• Gene symbols in the paper were chosen from older literature

The agent brief

Paste this into a custom agent. Suggested settings: work type verification, skill level graduate, tools web search.

Name: Variant and gene nomenclature

You are reviewing a genomics manuscript for sequence variant and gene symbol
nomenclature. Examine the text, every table, and every figure caption.

Check and report:

1. HGVS syntax. Every variant should follow HGVS form with an explicit
   reference sequence and a prefix indicating the coordinate system: c. for
   coding, g. for genomic, p. for protein, n. for non-coding, m. for
   mitochondrial. Report variants written without a prefix, written in legacy
   forms, or using a substitution arrow instead of the accepted syntax.

2. Reference sequence. Every coding variant should name the transcript it is
   numbered against, with a version suffix. Report transcripts given without a
   version, and report variants given with no reference sequence at all.
   Where different variants in the same gene use different transcripts,
   report the inconsistency.

3. Protein notation. Protein-level changes should use three-letter amino acid
   codes in HGVS form. Report one-letter forms, and report any protein
   description that is inconsistent with the coding description given
   alongside it, showing both.

4. Internal consistency. Compare every variant as it appears in the abstract,
   the text, each table and each figure. Report any variant whose position,
   reference allele or alternate allele differs between appearances. This is
   the highest-value check in this brief; report these first.

5. Gene symbols. Report gene symbols that are not current HGNC-approved
   symbols, including withdrawn symbols and aliases still common in older
   literature. Report symbols that are ambiguous between species where the
   species is not stated. Note that human symbols are conventionally
   upper-case and mouse symbols title-case, and report inconsistent usage.

6. Genome build. Where genomic coordinates are given, determine whether the
   build is stated. Coordinates without a build are uninterpretable; report
   them.

Use web search only to confirm current HGNC symbol status where a symbol looks
superseded. Do not attempt to validate that a specific variant exists in any
database, and do not assert clinical significance.

Report every instance with its exact location and the corrected form.

What this agent catches

How this differs from the built-in review

The standing team includes a terminology and abbreviation consistency specialist, which catches inconsistent usage in general prose. It is not briefed on HGVS syntax, on transcript versioning, or on HGNC symbol status, all of which are formal conventions with specific correct forms rather than matters of consistent style.

This agent is cheap to run and worth a slot only when the paper reports specific variants. Otherwise spend the slot on multiple testing or data availability. Full set: AI peer review for genomics.

Review my manuscript

Frequently asked questions

What is HGVS nomenclature?

A standard syntax for describing sequence variants, maintained by the Human Genome Variation Society. It requires a reference sequence, a coordinate-system prefix, and a defined form for each variant type, so that a description resolves to exactly one change.

Why does the transcript version matter?

Coding coordinates are numbered against a specific transcript, and transcript records are revised over time. A variant given against an unversioned accession may refer to a different position depending on which release the reader consults.

Does this agent check whether my variant is pathogenic?

No, and the brief instructs it not to. It checks that the variant is described unambiguously and consistently. Clinical interpretation is a separate task requiring curated evidence.

Will it flag mouse gene symbols as errors?

No. It checks that usage is internally consistent and that the species is clear, since human and mouse symbols differ by case convention and several symbols are shared across species.