Transiting thru Iran
 

OK, here is the situation - I have two citizenships, one from US and second - from a country with visa free visit of Iran.

Couple hours ago I was researching options on Skypicker to fly to Turkey from KUL and came some really weird route thru Tehran the price tag of less than $200 one way.

Could anyone tell what are implications if I will transit thru Iran, while taking but not showing my US passport and instead showing my second passport at checkpoint?

I don't it's a problem unless they ask directly about it. Just keep quiet and answer questions directly/honestly. Present the passport w/ visa free travel and you'll be good :D

Could a trip through Iran later prevent you from getting Global Entry or a job that requires a (USA) security clearance? In fact, what's the current rule on whether USA citizens are permitted (by the USA) to visit Iran?

No restrictions on visits for US citizens.

I already have GE. I don't understand why transiting thru Iran while NOT using US passport would endanger my GE status.

I don't see why it should. I visited Iran and got GE after the trip.

- Not volunteering info = advised
- Answering honestly if questioned specifically (including later, by U.S. authorities) = advised
- Lying = not advised
- Taking advice from internet strangers about legal matters = (hahahahaha)