SPTLC1, variants, traits, and what the research shows

SPTLC1 - what this gene does

Variants in SPTLC1 cluster almost entirely around neurological traits, with one variant also linked to a rare disease category. The consistent trait signal across its top-ranked variants places this gene squarely in the neurological research space.

Key takeaways

• Nearly all top-ranked variants in this gene are associated with neurological conditions
• One variant carries a rare disease association rather than a general neurological one
• All 20 highlighted variants share the same high magnitude score of 5.50
• These associations come from population-level studies, not individual predictions
• Detailed per-variant study data is not yet available, so effect size specifics cannot be reported

Notable variants

All 20 top-ranked variants carry a magnitude score of 5.50, a combined measure of effect size and evidence strength. Among the neurologically linked entries, rs119482082, rs139086093, rs142153571, rs143754785, and rs267607087 represent the first tier of signals tied to neurological traits. Standing apart from the neurological cluster, rs2538427518 is the only variant in this top-20 set classified under a rare disease trait, which may point to a more specific clinical condition distinct from the broader neurological grouping.

Trait associations

The dominant trait theme for this gene is neurological. Nineteen of the 20 top-ranked variants, including rs1478177125, rs1554706429, rs1554706430, rs199609730, rs200773661, rs147143593, rs369803886, rs745684683, rs748384890, rs748723735, rs750680286, rs764460003, rs765970732, and rs768841574, are classified under neurological traits. The single exception, rs2538427518, falls under rare disease. The concentration of neurological signals across 275 total catalogued variants reinforces this gene's presence in nervous system research.

Evidence quality

No individual SNP-level study summaries are yet on file for this gene, which means specific effect sizes such as odds ratios (a measure of how much a variant changes the odds of a trait) or beta coefficients (a measure of magnitude in continuous traits), sample sizes, and replication status cannot be reported for any single variant. What is available is a ranked list of 275 catalogued variants, with the 20 highlighted here all scoring a magnitude of 5.50. Magnitude scores reflect a combination of effect size and evidence strength, but without the underlying study data the exact basis for each score cannot be verified here. The neurological trait classification is consistent across virtually all top variants, which is a meaningful pattern, but the depth of the evidence base for individual variants remains to be documented in future SNP summaries.

What this is NOT

These variants are population-level statistical signals from studies such as GWAS (genome-wide association studies, which scan many people's genomes for variants statistically linked to a trait) and are not deterministic predictors for any individual. Nothing here constitutes a diagnosis, a prescription, or any form of medical advice.