CNTN4, variants, traits, and what the research shows

CNTN4 - what this gene does

Based on the variants catalogued here, CNTN4 shows up in genetic research across several trait themes - most prominently rare disease, but also neurological conditions, cancer, mental health, immune function, and kidney and cardiovascular traits.

Key takeaways

• The two highest-magnitude variants in this gene are both linked to rare disease
• Three separate variants point to neurological associations, making it the most internally replicated theme after rare disease
• Cancer, mental health, immune, kidney, and cardiovascular traits each appear across this gene's variant profile
• Magnitude scores of 4.50-5.50 indicate above-average signal strength across the dataset
• These are population-level associations and do not predict outcomes for any individual

Notable variants

The strongest signals come from rs200414214 and rs775725299, both scored at magnitude 5.50 and both flagged for rare disease - the highest-magnitude entries in this dataset. At magnitude 4.50, three variants - rs11713158, rs2619566, and rs57442028 - all carry neurological flags, representing the most internally consistent theme in the profile. Cancer associations appear in rs112113758 and rs75622279; mental health in rs17022006; immune traits in rs182265848; cardiovascular in rs72996095; and kidney traits in both rs35615064 and rs75585701.

Trait associations

The variant data on file spans six trait domains:

• Rare disease: the top two signals by magnitude - rs200414214 and rs775725299 - both fall here.
• Neurological: rs11713158, rs2619566, and rs57442028 all carry neurological flags at magnitude 4.50; three concordant signals within a single gene's profile provide mild internal corroboration.
• Cancer: rs112113758 and rs75622279 are both flagged for cancer-linked traits at magnitude 4.50; two variants pointing to the same domain modestly strengthens the signal.
• Mental health: rs17022006 is associated with a mental health trait.
• Immune: rs182265848 carries an immune-trait flag.
• Cardiovascular: rs72996095 is linked to a cardiovascular trait.
• Kidney: rs35615064 and rs75585701 are both flagged for kidney traits - two variants in the same domain adds mild corroboration.

Evidence quality

Of 202 variants on file for this gene, 19 carry prior research summaries; the entries highlighted above represent those with the highest magnitude scores. The two magnitude-5.50 rare-disease variants - rs200414214 and rs775725299 - carry the strongest individual signals in this dataset; high magnitude scores at this level typically reflect rarer variants with larger per-carrier effect sizes rather than common GWAS (genome-wide association study - a method that scans large populations for variants statistically linked to a trait) hits. The remaining highlighted variants sit at magnitude 4.50, consistent with well-evidenced but more moderate signals. No specific odds ratios, beta coefficients, or study sample sizes are available in the current dataset, so the strength of individual associations cannot be precisely quantified here. The neurological domain benefits from three concordant variant flags within this gene's profile, representing mild internal replication, but cross-cohort replication data are not reported for most entries.

What this is NOT

All variants listed here are population-level statistical signals from large genetic studies; they describe average tendencies across groups and are not deterministic predictors for any individual. Nothing on this page constitutes medical advice, a diagnosis, or a clinical recommendation.