ncbp-2
C. elegans
Nuclear cap-binding protein subunit 2
What the model saw
Gene: ncbp-2 Organism: Caenorhabditis elegans Known functions: Nuclear cap-binding protein subunit 2. RNA binding. RNA cap binding. nucleic acid binding.
View unredacted entry
Nuclear cap-binding protein subunit 2. RNA binding. RNA cap binding. nucleic acid binding.
Solver output
NCBP-2 is the small subunit of the nuclear cap-binding complex (CBC), which binds the 5' m7G cap of nascent pre-mRNAs and facilitates early steps of mRNA processing including splicing, 3' end formation, and nuclear export. While RNA processing quality is broadly important for proteostasis and gene expression fidelity, the CBC is a general, constitutive factor without a clear directional bias toward pro- or anti-longevity pathways. Its role in mRNA biogenesis could intersect with longevity-relevant pathways (e.g., DAF-16/FOXO target mRNA processing, stress response transcripts), but no specific longevity pathway is selectively regulated by NCBP-2 based on the available annotations. The function is too general to confidently assign a directional influence on lifespan.
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 "pro_longevity." The model's reasoning is logically sound given the available information - NCBP-2 is indeed a general RNA processing factor, and without specific experimental data linking it to longevity pathways, the model's uncertainty is understandable. However, the model failed to arrive at the correct answer. The mechanistic reasoning about CBC function is accurate but doesn't connect to the actual pro-longevity finding. The model's confidence of 0.38 reflects appropriate uncertainty, making this a case of being appropriately uncertain rather than confidently wrong. The reasoning quality is decent - the model correctly identifies the gene's function and acknowledges the potential connections to longevity pathways, but ultimately fails to commit to the correct direction.
Raw API responses
solver
{
"reasoning": "NCBP-2 is the small subunit of the nuclear cap-binding complex (CBC), which binds the 5' m7G cap of nascent pre-mRNAs and facilitates early steps of mRNA processing including splicing, 3' end formation, and nuclear export. While RNA processing quality is broadly important for proteostasis and gene expression fidelity, the CBC is a general, constitutive factor without a clear directional bias toward pro- or anti-longevity pathways. Its role in mRNA biogenesis could intersect with longevity-relevant pathways (e.g., DAF-16/FOXO target mRNA processing, stress response transcripts), but no specific longevity pathway is selectively regulated by NCBP-2 based on the available annotations. The function is too general to confidently assign a directional influence on lifespan.",
"confidence": 0.38,
"key_pathways": [
"nuclear cap-binding complex (CBC)",
"pre-mRNA processing and nuclear export",
"mRNA biogenesis"
],
"mechanism_class": "unclear",
"longevity_influence": "unclear"
}advisor
{
"notes": "The model predicted \"unclear\" while the ground truth is \"pro_longevity.\" The model's reasoning is logically sound given the available information - NCBP-2 is indeed a general RNA processing factor, and without specific experimental data linking it to longevity pathways, the model's uncertainty is understandable. However, the model failed to arrive at the correct answer. The mechanistic reasoning about CBC function is accurate but doesn't connect to the actual pro-longevity finding. The model's confidence of 0.38 reflects appropriate uncertainty, making this a case of being appropriately uncertain rather than confidently wrong. The reasoning quality is decent - the model correctly identifies the gene's function and acknowledges the potential connections to longevity pathways, but ultimately fails to commit to the correct direction.",
"failure_mode": "appropriately_uncertain",
"answer_correct": false,
"mechanism_correct": false,
"reasoning_quality": 3,
"ground_truth_questionable": false
}