Nomenclature
Overview
Nomenclature in genetics provides the standardized language used to describe chromosomal findings and sequence variants. This chapter covers two complementary systems: ISCN (International System for Human Cytogenomic Nomenclature) for cytogenetic results and HGVS (Human Genome Variation Society) for molecular sequence variants. Accurate use of nomenclature is essential for interpreting laboratory reports and communicating findings to other providers.
Nomenclature is a routine vocabulary skill used every time you read a laboratory report. Reading a karyotype string or HGVS variant description and translating it into the underlying genetic finding (or going the other direction) is bread-and-butter clinical practice. The key is familiarity with the conventions and practice reading real examples.
While memorizing every possible notation is not realistic, understanding the structure and logic of each system allows you to decode unfamiliar descriptions. ISCN follows a consistent pattern of total chromosome count, sex chromosomes, then abnormalities. HGVS uses a reference sequence prefix followed by a description of the change at the DNA, RNA, or protein level. Learning the common patterns and practicing with examples is the most effective study strategy.
Key Concepts
- ISCN karyotype format: total count, sex chromosomes, abnormalities (e.g., 46,XX,del(5)(p15.2))
- Common ISCN symbols: del, dup, inv, t, rob, der, +, -, mos, and how to read complex karyotypes
- HGVS DNA notation: c. (coding DNA), g. (genomic), m. (mitochondrial) with substitution, deletion, duplication, insertion syntax
- HGVS protein notation: p. notation using three-letter amino acid codes, frameshift, and nonsense descriptions
- Matching notation to variant type: being able to translate between a written description of a variant and its formal notation
Cytogenetic Nomenclature
ISCN is the standard system for describing karyotype results: numerical abnormalities (aneuploidies), structural abnormalities (translocations, deletions, duplications, inversions, ring chromosomes), mosaicism notation, and the conventions for derivative chromosomes. ISCN sits downstream of the Cytogenetic Techniques chapter: once you know how karyotype and FISH work, ISCN gives you the language to describe what was found.
Molecular Nomenclature
HGVS is the standard system for describing sequence-level variants: substitutions, deletions, duplications, insertions, and complex variants at the DNA, RNA, and protein levels. HGVS is the notation used on every molecular test report and is essential for reading those reports and communicating findings to other providers and patients.
Together, these two systems give you the complete vocabulary for describing genetic findings at both the chromosome and sequence level.