Can mthfr 2copies a1298c cause second trimester loss? Also, can low progesterone cause 2nd tri loss?

MTHFR. Defects in the mthfr gene can cause many health issues. For more information on how this gene mutation is affecting your health, read this... http://doccarnahan.blogspot.com/2013/10/whats-big-deal-about-methylation-update.html.
Not 1298. Mthfr 1298 is not known to be related to miscarriage. It causes reduced bh4, and thus can affect synthesis of neurotransmitters, which can then affect mood.
Probably not. I would look for another cause or accept that you may not find a cause. My pathology colleagues with whom i've spoken are concerned about the promoting of common mthfr variants found on screening as serious disease. If someone has told you something that alarms you, please talk with an independent physician or geneticist. I'm sorry for your loss and wish you the best.