Description
Parse a Ter-style protein stop-extension syntax subset; unknown distance is represented explicitly.
Pharmacogenomic records distinguish allele labels, copy counts, reference-sequence versions, coordinate systems, and evidence about chromosome phase. A balanced count or matching token can check a record without establishing the underlying genotype. Supplied activity values and interpretation rules remain separate from a current gene-specific clinical guideline.
Parse a Ter-style protein stop-extension syntax subset; unknown distance is represented explicitly.
When to use this tool
Use Pharmacogene Hgvs Stop Extension Token when you need this specific allele-token, reference-coordinate, copy-budget, or source-support check.
How to use the tool and how it works
- Enter token. Use the units and conventions below.
- Run the tool. Correct any format, range, or cross-field input error before interpreting the output.
- Read referenceStop, newResidue, distance, distanceKnown. Inspect distanceKnown before interpreting the associated values.
Parse p.Ter followed by a positive stop position, an uppercase letter and two lowercase letters for the new residue, then extTer and a positive distance or ?. Return referenceStop, newResidue, distance, and distanceKnown; unknown distance returns zero.1
| Input field | Meaning and units | Accepted input |
|---|---|---|
| token | Complete literal token in the grammar stated above. | Required. Text; maximum UTF-16 length 8192. |
| Output field | Interpretation | Returned shape |
|---|---|---|
| referenceStop | Reference Stop | Required. Safe integer. |
| newResidue | Three-letter-shaped token, not validated against amino-acid names. | Required. Text; maximum UTF-16 length 8192. |
| distance | Positive extension distance when distanceKnown; zero placeholder otherwise. | Required. Safe integer. |
| distanceKnown | Distance Known | Required. Boolean. |
{
"input": {
"token": "p.Ter110GlnextTer17"
},
"output": {
"referenceStop": 110,
"newResidue": "Gln",
"distance": 17,
"distanceKnown": true
}
}Limitations and assumptions
- The residue-shaped token is not checked against the amino-acid vocabulary and the reference sequence is not validated. This restricted stop-extension grammar is not a general HGVS protein parser; inspect distanceKnown before using zero.
- Inputs must satisfy both the field types and the cross-field conditions above. Invalid input causes an error; a successful false flag or documented placeholder is a different result.
Alternative or Complementary methods
Use a current gene-specific nomenclature and a validated interpretation process when allele identity, phase, function, or clinical decisions matter. Verify source versions and reference coordinates before combining records.
References
Similar or alternative tools
- Pharmacogenomic Variant Hgvs Prefix Token
Split a versioned HGVS accession prefix without validating the variant or reference sequence.
- Pharmacogene Hgvs Intronic Offset Sign
Parse a positive coding-position/intronic-offset subset without mapping it to a reference sequence.