vang-1
C. elegans
Vang-like protein
What the model saw
Gene: vang-1 Organism: Caenorhabditis elegans Known functions: Vang-like protein. PDZ domain binding.
View unredacted entry
Vang-like protein. PDZ domain binding.
Solver output
vang-1 encodes the C. elegans ortholog of Van Gogh/Vangl, a core component of the planar cell polarity (PCP) signaling pathway. Its PDZ domain binding activity mediates protein-protein interactions critical for PCP complex assembly and Wnt/PCP non-canonical signaling. While Wnt signaling broadly influences aging and stem cell maintenance, the specific role of PCP/Vangl in longevity is not well established in C. elegans. PDZ domain binding is a scaffolding function that could modulate intercellular communication, but there is insufficient evidence to assign a clear pro- or anti-longevity direction based solely on these annotations.
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 correctly identified vang-1 as a Van Gogh/Vangl ortholog involved in PCP/Wnt signaling, but failed to assign the correct longevity direction. The reasoning is plausible but ultimately non-committal. The model's uncertainty is understandable given limited published data on vang-1's specific role in C. elegans longevity, but the answer is still incorrect. The mechanism class of "altered_intercellular_communication" is a reasonable guess but not confirmed as correct for the anti-longevity mechanism.
Raw API responses
solver
{
"reasoning": "vang-1 encodes the C. elegans ortholog of Van Gogh/Vangl, a core component of the planar cell polarity (PCP) signaling pathway. Its PDZ domain binding activity mediates protein-protein interactions critical for PCP complex assembly and Wnt/PCP non-canonical signaling. While Wnt signaling broadly influences aging and stem cell maintenance, the specific role of PCP/Vangl in longevity is not well established in C. elegans. PDZ domain binding is a scaffolding function that could modulate intercellular communication, but there is insufficient evidence to assign a clear pro- or anti-longevity direction based solely on these annotations.",
"confidence": 0.35,
"key_pathways": [
"Wnt/planar cell polarity (PCP) signaling",
"PDZ domain-mediated protein scaffolding",
"non-canonical Wnt signaling"
],
"mechanism_class": "altered_intercellular_communication",
"longevity_influence": "unclear"
}advisor
{
"notes": "The model predicted \"unclear\" with low confidence (0.35), while the ground truth is \"anti_longevity.\" The model correctly identified vang-1 as a Van Gogh/Vangl ortholog involved in PCP/Wnt signaling, but failed to assign the correct longevity direction. The reasoning is plausible but ultimately non-committal. The model's uncertainty is understandable given limited published data on vang-1's specific role in C. elegans longevity, but the answer is still incorrect. The mechanism class of \"altered_intercellular_communication\" is a reasonable guess but not confirmed as correct for the anti-longevity mechanism.",
"failure_mode": "appropriately_uncertain",
"answer_correct": false,
"mechanism_correct": false,
"reasoning_quality": 2,
"ground_truth_questionable": false
}