y46g5a.20
C. elegans
Nuclear receptor domain-containing protein
What the model saw
Gene: Y46G5A.20 Organism: Caenorhabditis elegans Known functions: Nuclear receptor domain-containing protein. protein binding.
View unredacted entry
Nuclear receptor domain-containing protein. protein binding.
Solver output
Y46G5A.20 encodes a nuclear receptor domain-containing protein in C. elegans. Nuclear receptors are ligand-activated transcription factors that regulate diverse biological processes; in C. elegans, some nuclear receptors (e.g., DAF-12, NHR-49) are well-characterized modulators of longevity through lipid metabolism and dauer/IIS pathways, while others have no known role in aging. The annotation "protein binding" is too generic to specify a downstream effector pathway. Without knowing the specific ligand, target genes, or pathway context for this uncharacterized NHR, it is impossible to determine whether its activity promotes or opposes longevity. The nuclear receptor superfamily in C. elegans is large (~284 members), and the majority remain functionally uncharacterized, making a directional prediction unreliable.
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), while the ground truth is "anti_longevity." The model's reasoning is sound in noting that C. elegans has ~284 nuclear receptors and most are uncharacterized, making directional prediction difficult. However, the model failed to commit to a prediction and missed the anti-longevity classification. The mechanistic reasoning is generic and doesn't identify the specific anti-longevity mechanism. The model's uncertainty is understandable given the limited annotation, but it still got the answer wrong. The reasoning quality is moderate - it correctly identifies the nuclear receptor family context and relevant pathways but doesn't arrive at the correct conclusion.
Raw API responses
solver
{
"reasoning": "Y46G5A.20 encodes a nuclear receptor domain-containing protein in C. elegans. Nuclear receptors are ligand-activated transcription factors that regulate diverse biological processes; in C. elegans, some nuclear receptors (e.g., DAF-12, NHR-49) are well-characterized modulators of longevity through lipid metabolism and dauer/IIS pathways, while others have no known role in aging. The annotation \"protein binding\" is too generic to specify a downstream effector pathway. Without knowing the specific ligand, target genes, or pathway context for this uncharacterized NHR, it is impossible to determine whether its activity promotes or opposes longevity. The nuclear receptor superfamily in C. elegans is large (~284 members), and the majority remain functionally uncharacterized, making a directional prediction unreliable.",
"confidence": 0.35,
"key_pathways": [
"nuclear receptor signaling",
"lipid metabolism / NHR pathway",
"DAF-12/dauer signaling"
],
"mechanism_class": "deregulated_nutrient_sensing",
"longevity_influence": "unclear"
}advisor
{
"notes": "The model predicted \"unclear\" with low confidence (0.35), while the ground truth is \"anti_longevity.\" The model's reasoning is sound in noting that C. elegans has ~284 nuclear receptors and most are uncharacterized, making directional prediction difficult. However, the model failed to commit to a prediction and missed the anti-longevity classification. The mechanistic reasoning is generic and doesn't identify the specific anti-longevity mechanism. The model's uncertainty is understandable given the limited annotation, but it still got the answer wrong. The reasoning quality is moderate - it correctly identifies the nuclear receptor family context and relevant pathways but doesn't arrive at the correct conclusion.",
"failure_mode": "appropriately_uncertain",
"answer_correct": false,
"mechanism_correct": false,
"reasoning_quality": 3,
"ground_truth_questionable": false
}