Dmd
M. musculus
dystrophin, muscular dystrophy
What the model saw
Gene: Dmd Organism: Mus musculus Known functions: dystrophin, muscular dystrophy. dystrophin. PDZ domain binding. actin binding. dystroglycan binding. integrin binding. lamin binding. myosin binding. nitric-oxide synthase binding. protein binding. protein-containing complex binding. structural constituent of muscle. vinculin binding. zinc ion binding.
View unredacted entry
dystrophin, muscular dystrophy. dystrophin. PDZ domain binding. actin binding. dystroglycan binding. integrin binding. lamin binding. myosin binding. nitric-oxide synthase binding. protein binding. protein-containing complex binding. structural constituent of muscle. vinculin binding. zinc ion binding.
Solver output
Dystrophin (Dmd) is the structural scaffold protein of the dystrophin-associated protein complex (DAPC) at the sarcolemma, linking the intracellular actin cytoskeleton to the extracellular matrix via dystroglycan and integrins. Loss of dystrophin causes progressive muscle membrane fragility, repeated cycles of degeneration and regeneration, and eventual exhaustion of muscle satellite stem cells — a canonical hallmark of aging-related stem cell depletion. Additionally, dystrophin's binding to neuronal nitric-oxide synthase (nNOS) is critical for muscle metabolic signaling; its absence leads to mitochondrial dysfunction and oxidative stress in muscle fibers. The chronic inflammatory milieu driven by dystrophin deficiency (as in mdx mice) accelerates tissue aging phenotypes. Because the normal function of Dmd is to maintain sarcolemmal integrity and preserve the regenerative capacity of muscle, its presence is pro-homeostatic, meaning its loss (or dysfunction) is anti-longevity; thus the gene's normal function opposes aging/promotes longevity.
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 correctly identifies the mechanistic role of Dmd (sarcolemmal integrity, DAPC, nNOS signaling, stem cell maintenance) and even correctly concludes that Dmd's normal function is pro-homeostatic/pro-longevity. However, the model then contradicts itself by labeling the gene as "anti_longevity" in its final prediction, when the ground truth is "pro_longevity." The reasoning explicitly states "its presence is pro-homeostatic, meaning its loss (or dysfunction) is anti-longevity; thus the gene's normal function opposes aging/promotes longevity" — which should lead to a pro_longevity classification. The model appears to have confused the effect of gene loss vs. gene presence when assigning the final label, despite correctly reasoning through the mechanism. This is a classification error where the model's stated conclusion in the reasoning contradicts its final answer field.
Raw API responses
solver
{
"reasoning": "Dystrophin (Dmd) is the structural scaffold protein of the dystrophin-associated protein complex (DAPC) at the sarcolemma, linking the intracellular actin cytoskeleton to the extracellular matrix via dystroglycan and integrins. Loss of dystrophin causes progressive muscle membrane fragility, repeated cycles of degeneration and regeneration, and eventual exhaustion of muscle satellite stem cells — a canonical hallmark of aging-related stem cell depletion. Additionally, dystrophin's binding to neuronal nitric-oxide synthase (nNOS) is critical for muscle metabolic signaling; its absence leads to mitochondrial dysfunction and oxidative stress in muscle fibers. The chronic inflammatory milieu driven by dystrophin deficiency (as in mdx mice) accelerates tissue aging phenotypes. Because the normal function of Dmd is to maintain sarcolemmal integrity and preserve the regenerative capacity of muscle, its presence is pro-homeostatic, meaning its loss (or dysfunction) is anti-longevity; thus the gene's normal function opposes aging/promotes longevity.",
"confidence": 0.72,
"key_pathways": [
"dystrophin-associated protein complex (DAPC) / sarcolemmal integrity",
"nNOS-mediated nitric oxide signaling in muscle",
"muscle satellite cell regeneration and stem cell maintenance"
],
"mechanism_class": "stem_cell_exhaustion",
"longevity_influence": "anti_longevity"
}advisor
{
"notes": "The model correctly identifies the mechanistic role of Dmd (sarcolemmal integrity, DAPC, nNOS signaling, stem cell maintenance) and even correctly concludes that Dmd's normal function is pro-homeostatic/pro-longevity. However, the model then contradicts itself by labeling the gene as \"anti_longevity\" in its final prediction, when the ground truth is \"pro_longevity.\" The reasoning explicitly states \"its presence is pro-homeostatic, meaning its loss (or dysfunction) is anti-longevity; thus the gene's normal function opposes aging/promotes longevity\" — which should lead to a pro_longevity classification. The model appears to have confused the effect of gene loss vs. gene presence when assigning the final label, despite correctly reasoning through the mechanism. This is a classification error where the model's stated conclusion in the reasoning contradicts its final answer field.",
"failure_mode": "right_answer_wrong_reasoning",
"answer_correct": false,
"mechanism_correct": true,
"reasoning_quality": 3,
"ground_truth_questionable": false
}