ifa-3
C. elegans
Intermediate filament protein ifa-3
What the model saw
Gene: ifa-3 Organism: Caenorhabditis elegans Known functions: Intermediate filament protein ifa-3. structural constituent of cytoskeleton.
View unredacted entry
Intermediate filament protein ifa-3. structural constituent of cytoskeleton.
Solver output
IFA-3 is a C. elegans intermediate filament protein that serves as a structural constituent of the cytoskeleton. Intermediate filaments provide mechanical integrity to cells, but their direct role in aging pathways is not well-established. While cytoskeletal integrity is important for cellular homeostasis, intermediate filament proteins in C. elegans (particularly intestinal IFPs) have been linked to stress responses and proteostasis, but the specific contribution of ifa-3 to longevity is not clearly mapped to a canonical pro- or anti-longevity pathway. The molecular function annotation alone (structural cytoskeletal role) does not unambiguously place this gene in a known aging hallmark pathway such as nutrient sensing, proteostasis, or mitochondrial function.
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" while the ground truth is "anti_longevity." The model was appropriately uncertain given the limited information provided (only structural cytoskeletal function annotation), but it still got the answer wrong. The reasoning is generic and doesn't identify any specific mechanism by which ifa-3 would be anti-longevity. The model correctly noted that cytoskeletal integrity relates to cellular homeostasis but couldn't commit to a direction. With only the structural annotation provided, the uncertainty is understandable, but the model should have perhaps leaned toward anti_longevity given that loss of structural cytoskeletal components often reduces fitness/longevity. The confidence of 0.35 reflects appropriate uncertainty but the prediction is still incorrect.
Raw API responses
solver
{
"reasoning": "IFA-3 is a C. elegans intermediate filament protein that serves as a structural constituent of the cytoskeleton. Intermediate filaments provide mechanical integrity to cells, but their direct role in aging pathways is not well-established. While cytoskeletal integrity is important for cellular homeostasis, intermediate filament proteins in C. elegans (particularly intestinal IFPs) have been linked to stress responses and proteostasis, but the specific contribution of ifa-3 to longevity is not clearly mapped to a canonical pro- or anti-longevity pathway. The molecular function annotation alone (structural cytoskeletal role) does not unambiguously place this gene in a known aging hallmark pathway such as nutrient sensing, proteostasis, or mitochondrial function.",
"confidence": 0.35,
"key_pathways": [
"cytoskeletal integrity",
"intermediate filament network",
"cellular mechanical homeostasis"
],
"mechanism_class": "other",
"longevity_influence": "unclear"
}advisor
{
"notes": "The model predicted \"unclear\" while the ground truth is \"anti_longevity.\" The model was appropriately uncertain given the limited information provided (only structural cytoskeletal function annotation), but it still got the answer wrong. The reasoning is generic and doesn't identify any specific mechanism by which ifa-3 would be anti-longevity. The model correctly noted that cytoskeletal integrity relates to cellular homeostasis but couldn't commit to a direction. With only the structural annotation provided, the uncertainty is understandable, but the model should have perhaps leaned toward anti_longevity given that loss of structural cytoskeletal components often reduces fitness/longevity. The confidence of 0.35 reflects appropriate uncertainty but the prediction is still incorrect.",
"failure_mode": "appropriately_uncertain",
"answer_correct": false,
"mechanism_correct": false,
"reasoning_quality": 2,
"ground_truth_questionable": false
}