ISCN pedigree symbols: reference guide and relationship to clinical cytogenomics

Short version. ISCN (International System for Human Cytogenomic Nomenclature) is the primary standard for describing human chromosomal and cytogenomic findings — karyotypes, copy-number variants, and molecular cytogenomic results. ISCN itself focuses on cytogenomic language rather than pedigree symbols, but the two are routinely used together: a clinical pedigree drawn in the widely used NSGC symbol set records who in the family has had cytogenomic testing, and ISCN nomenclature describes the result for each tested individual. Because the terms are often used interchangeably in day-to-day practice, "ISCN pedigree symbols" is a common search phrase for the clinical pedigree convention that sits alongside ISCN reporting. This page clarifies the relationship and gives the symbol reference.

ISCN in one paragraph

ISCN is maintained by an international standing committee and periodically updated. It defines the notation for karyotype descriptions (for example, 46,XX or 47,XY,+21 for Down syndrome), structural rearrangements, fluorescence in situ hybridisation (FISH) results, array comparative genomic hybridisation (aCGH) findings, and sequence-level cytogenomic findings. Its purpose is to ensure that a chromosomal finding written in one laboratory is interpretable by any cytogeneticist elsewhere.

ISCN does not formally define the shapes used in pedigree diagrams; those are the province of NSGC standards. But in routine clinical communication the distinction is often blurred, and "ISCN-style pedigree" is shorthand for a clinical pedigree drawn with standard symbols and annotated with ISCN cytogenomic results.

Symbol reference — the conventions used alongside ISCN

The same symbol set is used whether the pedigree is drawn by hand or rendered by software. For more detail on the specific NSGC recommendations, see our NSGC pedigree notation reference.

ISCN annotations on a pedigree

When a pedigree individual has been tested cytogenetically, the ISCN result is recorded beside the symbol. Common forms include:

• Normal karyotype: 46,XX or 46,XY.
• Trisomy: 47,XY,+21 for Down syndrome; 47,XY,+18 for Edwards syndrome; 47,XY,+13 for Patau syndrome.
• Sex chromosome aneuploidy: 47,XXY for Klinefelter syndrome; 45,X for Turner syndrome; 47,XYY; 47,XXX.
• Translocations: 46,XY,t(11;22)(q23;q11.2) for the familial constitutional Emanuel syndrome translocation.
• Microdeletions and microduplications: described via ISCN arr notation for array findings, for example arr[GRCh38] 22q11.21(18912231_21465672)x1 for a 22q11.2 deletion.
• Mosaic results: 47,XX,+21[15]/46,XX[10] for a 60/40 trisomy 21 mosaic.

These annotations are attached to the individual on the pedigree, not replacing the symbol. A female with Turner syndrome is still represented by a circle (sex assigned at birth) with 45,X and any relevant clinical annotation noted alongside.

Pedigree and karyogram in the same record

Clinical genetics services increasingly present the pedigree and the karyogram as complementary views of the same underlying data. The pedigree shows relationships and who was tested; the karyogram visualises the tested individual's chromosomes. In practice:

• Familial chromosomal rearrangements (balanced translocations, inversions) are inherited with patterns that look Mendelian on the pedigree. Recording the ISCN description on each carrier individual allows segregation to be traced visually.
• De novo chromosomal events in a proband are common in severe developmental conditions; annotating the proband with the ISCN result and the parental results as normal (for example, 46,XY and 46,XX in the parents) makes the de novo nature explicit.
• Microdeletion syndromes with variable penetrance may show a mixed pedigree with unaffected carrier parents and affected offspring; ISCN annotation clarifies the finding for each relative.
• Mosaicism has particular implications for reproductive counselling and is worth recording precisely on the pedigree.

Where ISCN ends and other nomenclatures begin

ISCN covers chromosomal and some molecular cytogenomic findings. Other nomenclature systems cover related territory:

• HGVS: for sequence-level variants (for example, NM_000492.3:c.1521_1523delCTT for the CFTR F508del variant).
• HGNC: for gene symbols.
• HPO: for standardised phenotype terms.
• OMIM: for disease entries.
• ICD-10: for clinical coding.

A good clinical record carries the right nomenclature for each finding. The pedigree is the hub; the ISCN, HGVS, HPO, OMIM, and ICD-10 annotations attach to the relevant individual.

How Evagene supports this

Evagene uses the pedigree symbol conventions that sit alongside ISCN reporting, enforcing them consistently across the pedigree. Each individual on the pedigree can carry structured annotations — ICD-10 codes for clinical coding, OMIM identifiers for disease entries, HGVS-compatible variant notation, and ISCN karyotype descriptions where available. The annotations travel with the pedigree through import and export, and are visible on the rendered diagram and in the underlying data model.

Evagene also includes a karyogram viewer that uses ISCN chromosomal nomenclature. When an individual has ISCN-annotated cytogenomic findings, the karyogram visualises the relevant chromosomes and the identified changes, providing a cytogenetic view alongside the pedigree view. This is particularly useful for familial translocations and microdeletion syndromes where the pedigree and the karyotype together give a fuller clinical picture than either alone.

Because the notation is software-enforced, pedigrees are presented in a uniform ISCN-consistent style regardless of how or by whom they were drawn. PDF, PNG, and SVG exports preserve the symbol set and annotations, and the REST API exposes the structured data for downstream systems that need both the pedigree and the ISCN descriptions.

Frequently asked questions

Related reading

• NSGC pedigree notation
• How to draw a pedigree chart
• Gender-inclusive pedigree drawing
• Pedigree drawing software
• Clinical genetics pedigree tools