  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 $\alpha\approx 5\times10^{-8}$ may be
present in the system.
