MySql UPDATE of tiny table is costly (0.2sec) - how to analyse further
Your innodb system variables indicate the innodb buffer pool is at 128M (the default). Its quite possible that the slowness of this single PK based update was due to this table not being in the innodb buffer pool. Look at the SHOW GLOBAL STATUS LIKE 'innodb_buffer_pool%' and adjust the pool size up until the Innodb_buffer_pool_reads vs Innodb_buffer_pool_read_requests is very small (&lt;1%).
This will be the case if 128M of more recently used innodb tables are in memory.
Another potential cause if there is a significant amount of write activity on the the server the innodb flushing /writing could be causing a delay because of storage limits.
If a f{data}sync of the disk can take 0.2 seconds occasionally that could correspond to the query time.