CNTNAP2, variants, traits, and what the research shows

CNTNAP2 - what this gene does

CNTNAP2 (Contactin-Associated Protein-Like 2, also known as CASPR2) is a gene whose catalogued variants associate with neurological conditions, rare diseases, and mental health traits. Without detailed per-variant study summaries currently available, what the data consistently show is that this gene sits at the intersection of brain and nervous system biology across all three of these broad domains.

Key takeaways

• CNTNAP2 variants are associated with three trait categories: neurological conditions, rare diseases, and mental health.
• The top-ranked variants all reach a magnitude score of 5.50, indicating high potential clinical relevance in curated variant databases.
• Neurological traits are the dominant signal: 15 of the top 20 variants by magnitude fall in this category.
• These are population-level statistical signals - not deterministic predictors for any individual.
• Detailed per-variant study data are not yet available; trait categories here reflect preliminary classification.

Notable variants

All 20 of the highest-ranked variants on file carry a magnitude of 5.50, the top tier in this dataset. On the neurological side, rs1057520468, rs1064794765, rs117876038, and rs1220885838 represent the strongest neurological-category entries. Rare disease associations at this same magnitude tier are carried by rs1057520549, rs1057520743, and rs1064796221. A mental health-linked variant, rs121908445, also reaches this top magnitude level - notable because it indicates the gene's research footprint extends beyond purely neurological classifications into psychiatric trait space as well.

Trait associations

Neurological traits account for 15 of the top 20 variants by magnitude, a concentration that recurs across many independent entries including rs138481453, rs138517537, rs139180845, rs141078449, rs141439475, rs141772824, rs141831869, rs142331907, rs142434274, rs143226012, and rs143286960. The repeated appearance of neurological-category variants across this many distinct rsids strengthens the inference that this gene has a consistent role in brain or nervous system biology, even before individual variant details are available. Rare disease associations (rs1057520549, rs1057520743, rs1064796221) and the mental health association (rs121908445) round out the picture with signals from adjacent domains.

Evidence quality

No per-variant research summaries are currently available for this gene in this dataset, which means specific effect sizes, odds ratios, sample sizes, and cohort replication status cannot be reported here. The 1,126 total variants on file - 36 of which are flagged for future detailed summary review - reflect a broad but incompletely characterized landscape. All 20 top-ranked variants carry magnitude 5.50; in curated variant databases such as ClinVar, high magnitude scores often correspond to pathogenic or likely-pathogenic classifications, but this interpretation cannot be confirmed without the underlying primary source data. All trait associations presented here should be treated as preliminary category-level signals until individual SNP pages are populated with study-level evidence.

What this is NOT

Every variant listed here represents a population-level statistical signal - the kind identified across large genomic studies - and none of these signals deterministically predicts health outcomes for any individual person. Nothing on this page constitutes medical advice, a clinical diagnosis, or a recommendation to take any action.