I assumed that the GSM module is working with 3V3 logic directly to the J50. On the J50 port pins D6 and D7 are 5v tolerant, but you'll only get 3V3 output on the TXD signal. That's probably OK, but I don't know what the GSM requires.
If you use one of the USB-serial adapters make sure that you use one that's compatible with your logic levels.
thank you for your advice. issue got solved.
there was some problem with the GSM module itself. I connected a pl2303 based usb-serial dongle and found that module was not responding to commands but J50 was indeed sending commands, I removed the module and soldered a new one and its working now.