YSC84
S. cerevisiae
Ysc84p
What the model saw
Gene: YSC84 Organism: Saccharomyces cerevisiae Known functions: Ysc84p. actin filament binding. phosphatidylinositol binding. protein binding.
View unredacted entry
Ysc84p. actin filament binding. phosphatidylinositol binding. protein binding.
Solver output
YSC84 encodes an actin-binding protein that also binds phosphatidylinositol lipids, placing it at the intersection of actin cytoskeleton regulation and membrane phosphoinositide signaling. In yeast, actin dynamics are important for endocytosis, autophagy, and vacuolar function, all of which can influence aging. However, Ysc84p is a member of the Lsb/SH3 adaptor family involved in actin patch assembly at endocytic sites, and its specific role in longevity-relevant pathways (e.g., autophagy flux, TOR signaling, or mitochondrial quality control) is not directly implied by these annotations alone. The phosphatidylinositol binding activity could link it to PI(4,5)P2-dependent endocytic regulation, but whether this promotes or opposes longevity is ambiguous. The generic "protein binding" annotation adds no mechanistic specificity. Without clearer evidence connecting Ysc84p to a defined pro- or anti-longevity pathway, a confident directional prediction cannot be made.
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 "unclear" with low confidence (0.35), but the ground truth is "anti_longevity." The model's reasoning about actin dynamics, endocytosis, and phosphoinositide signaling is plausible but doesn't arrive at the correct directional conclusion. The model was appropriately uncertain given the limited functional annotations provided, but it still got the answer wrong. The mechanistic reasoning is generic and doesn't specifically identify why YSC84 would be anti-longevity. This is a case where the model's uncertainty was somewhat justified by the sparse information, but the ground truth is definitive.
Raw API responses
solver
{
"reasoning": "YSC84 encodes an actin-binding protein that also binds phosphatidylinositol lipids, placing it at the intersection of actin cytoskeleton regulation and membrane phosphoinositide signaling. In yeast, actin dynamics are important for endocytosis, autophagy, and vacuolar function, all of which can influence aging. However, Ysc84p is a member of the Lsb/SH3 adaptor family involved in actin patch assembly at endocytic sites, and its specific role in longevity-relevant pathways (e.g., autophagy flux, TOR signaling, or mitochondrial quality control) is not directly implied by these annotations alone. The phosphatidylinositol binding activity could link it to PI(4,5)P2-dependent endocytic regulation, but whether this promotes or opposes longevity is ambiguous. The generic \"protein binding\" annotation adds no mechanistic specificity. Without clearer evidence connecting Ysc84p to a defined pro- or anti-longevity pathway, a confident directional prediction cannot be made.",
"confidence": 0.35,
"key_pathways": [
"actin cytoskeleton dynamics",
"phosphoinositide signaling",
"endocytosis"
],
"mechanism_class": "unclear",
"longevity_influence": "unclear"
}advisor
{
"notes": "The model predicted \"unclear\" with low confidence (0.35), but the ground truth is \"anti_longevity.\" The model's reasoning about actin dynamics, endocytosis, and phosphoinositide signaling is plausible but doesn't arrive at the correct directional conclusion. The model was appropriately uncertain given the limited functional annotations provided, but it still got the answer wrong. The mechanistic reasoning is generic and doesn't specifically identify why YSC84 would be anti-longevity. This is a case where the model's uncertainty was somewhat justified by the sparse information, but the ground truth is definitive.",
"failure_mode": "appropriately_uncertain",
"answer_correct": false,
"mechanism_correct": false,
"reasoning_quality": 2,
"ground_truth_questionable": false
}