SNX41
S. cerevisiae
Snx41p
What the model saw
Gene: SNX41 Organism: Saccharomyces cerevisiae Known functions: Snx41p. phosphatidylinositol binding. phosphatidylinositol-3-phosphate binding. protein binding.
View unredacted entry
Snx41p. phosphatidylinositol binding. phosphatidylinositol-3-phosphate binding. protein binding.
Solver output
SNX41 is a sorting nexin in S. cerevisiae that binds phosphatidylinositol-3-phosphate (PI3P), a lipid enriched on endosomal and autophagosomal membranes that is a key signal for autophagy and endosomal sorting. Sorting nexins with PX domains that bind PI3P are typically involved in cargo recognition and vesicle trafficking through the endosomal-lysosomal (vacuolar) pathway, including selective autophagy routes such as the Cvt pathway or mitophagy. Proper endosomal sorting and autophagic flux are essential for proteostasis and organelle quality control, both of which are critical determinants of replicative and chronological lifespan in yeast. Loss of PI3P-binding sorting nexins can impair vacuolar delivery of damaged proteins and organelles, accelerating aging. SNX41 has been specifically implicated in the selective autophagy of the Ego complex and TORC1 regulation at the vacuolar membrane, linking it to nutrient sensing and longevity pathways.
GenAge curators classify each gene's normal function as promoting (Pro-Longevity) or opposing (Anti-Longevity) longevity, based on synthesis across studies. Loss-of-function effects can vary from this depending on the manipulation.
Advisor judgment
The model predicted pro_longevity but the ground truth is anti_longevity. The model's reasoning about SNX41's role in PI3P binding, endosomal sorting, and autophagy is plausible in general terms, but it incorrectly concludes that loss of SNX41 would impair vacuolar delivery and accelerate aging (pro_longevity logic). In reality, SNX41 is anti_longevity, meaning its deletion extends lifespan. The model's mechanistic reasoning about TORC1 regulation is speculative and not well-supported. The model had moderate confidence (0.55) but still got the direction wrong. The reasoning quality is low because it built a narrative that led to the wrong conclusion, and the specific claim about SNX41 regulating the Ego complex/TORC1 appears to be hallucinated or confused with other sorting nexins.
Raw API responses
solver
{
"reasoning": "SNX41 is a sorting nexin in S. cerevisiae that binds phosphatidylinositol-3-phosphate (PI3P), a lipid enriched on endosomal and autophagosomal membranes that is a key signal for autophagy and endosomal sorting. Sorting nexins with PX domains that bind PI3P are typically involved in cargo recognition and vesicle trafficking through the endosomal-lysosomal (vacuolar) pathway, including selective autophagy routes such as the Cvt pathway or mitophagy. Proper endosomal sorting and autophagic flux are essential for proteostasis and organelle quality control, both of which are critical determinants of replicative and chronological lifespan in yeast. Loss of PI3P-binding sorting nexins can impair vacuolar delivery of damaged proteins and organelles, accelerating aging. SNX41 has been specifically implicated in the selective autophagy of the Ego complex and TORC1 regulation at the vacuolar membrane, linking it to nutrient sensing and longevity pathways.",
"confidence": 0.55,
"key_pathways": [
"PI3P-mediated endosomal sorting",
"selective autophagy / vacuolar trafficking",
"TORC1 nutrient sensing at the vacuole"
],
"mechanism_class": "disabled_macroautophagy",
"longevity_influence": "pro_longevity"
}advisor
{
"notes": "The model predicted pro_longevity but the ground truth is anti_longevity. The model's reasoning about SNX41's role in PI3P binding, endosomal sorting, and autophagy is plausible in general terms, but it incorrectly concludes that loss of SNX41 would impair vacuolar delivery and accelerate aging (pro_longevity logic). In reality, SNX41 is anti_longevity, meaning its deletion extends lifespan. The model's mechanistic reasoning about TORC1 regulation is speculative and not well-supported. The model had moderate confidence (0.55) but still got the direction wrong. The reasoning quality is low because it built a narrative that led to the wrong conclusion, and the specific claim about SNX41 regulating the Ego complex/TORC1 appears to be hallucinated or confused with other sorting nexins.",
"failure_mode": "confident_wrong",
"answer_correct": false,
"mechanism_correct": false,
"reasoning_quality": 2,
"ground_truth_questionable": false
}