Malzahar Runes explained
There's one set of runes for Malzahar on patch 15.1 that is the clear favorite for LoL players and pros alike. The best Malzahar rune paths on the position 
Top are 
Sorcery as the primary path and 
Precision as the secondary path with a pick rate of 50%. Besides picking runes on Malzahar you should learn how to play Malzahar and if you are interested in pro matches take a look on how a pro builds Malzahar. If you want to discuss 
Malzahar then you should visit the champion subreddit.
Malzahar runes from primary path
Sorcery empoweres abilities of Malzahar and increases the available champion resources. Most of high elo players – and our LoL pros in the the major regions – have agreed that 
Summon Aery is the best keystone rune to run on Malzahar. This keystone rune adds more poke damage to your abilities. And additionally grants an extra shield, whenever Malzahar empowers or protects an ally with abilities. Other primary runes on Malzahar are 
Manaflow Band, 
Transcendence and 
Scorch.
This is usually followed up by taking Manaflow Band for additional mana and mana regenaration. Transcendence for some more Ability Haste. Scorch increases your control in the early game.
Malzahar runes from secondary path
When it comes to your secondary path, most Malzahar players prefer to go with Precision. Precision improves attack and sustained damage on Malzahar troughout the match. On the Precision path, the best runes for Malzahar are 
Coup de Grace and 
Presence of Mind.
Malzahar deals with Coup de Grace more damage to targets with low health. Presence of Mind helps Malzahar with the mana problems by restoring missing mana, if a champion is killed.
FAQ for Malzahar Runes
Which is the best keystone rune on Malzahar?
The best keystone rune on Malzahar is Summon Aery. This Malzahar runes setup is then referred as Malzahar Summon Aery.
What runes does Malzahar use?
Runes from the paths Sorcery and Precision are the most used runes on Malzahar. For the exact pick rates of Malzahar runes used, you have to study the rune distribution presented.