The pulsar J1203+0038 rotates with a frequency \nu \approx 592 Hz and has been observed to transition between a radio state , during which it is visible as a millisecond radio pulsar , and and a Low Mass X-ray Binary state , during which accretion powered X-ray pulsations are visible . Timing during the two phases reveals that during the LMXB phase the neutron star is spinning down at a rate of \dot { \nu } \approx - 3 \times 10 ^ { -15 } Hz/s , which is approximately 27 % faster than the rate measured during the radio phase , \dot { \nu } \approx - 2.4 \times 10 ^ { -15 } Hz/s , and at odds with the predictions of accretion models . In this letter we suggest that the increase in spin-down rate is compatible with gravitational wave emission , and in particular to the creation of a ‘ mountain ’ during the accretion phase . We show that asymmetries in pycno-nuclear reaction rates in the crust can lead to a large enough mass quadrupole to explain the observed spin-down rate , which so far has no other self-consistent explanation , and that radio timing at the onset of the next millisecond radio pulsar phase can test this scenario . Another possibility is that an unstable r -mode with amplitude \alpha \approx 5 \times 10 ^ { -8 } may be present in the system .