its?

Yes.

No, I don't think so.

The impairment of the molecular pathway is implicated in depression as well as other disorders.
The gene inactivates it.

So "its" in this case looks like it refers to the pathway.

I agree with McT, and, in fact, i'd say that that is obvious.

Thank you all.

I agree, McTag. I was mistaken.

The gene inactivates a molecular pathway.

It [the molecular pathway] is crucial to the survival and function of neurons.

its impairment has been implicated in depression as well as other disorders.

The gene inactivates a molecular pathway which is crucial to the survival and function of neurons and whose impairment has been implicated in depression as well as other disorders.