Thank you folks for getting back.
@Simone3, yes this issue comes out as read timeout from the shard holding the system_properties table (there is only 1 partition for system_properties unreplicated).
We've used below workarounds to bypass it for now (the code change required in janusgraph is under test right now) based on the observations
- set the gc_grace_seconds for system_properties to 0
- truncate system_properties table periodically (say 2 hours)