Full back Aled Thomas (Newport/Dragons Academy), wing Aled Brew (Neath/Ospreys Academy) and flanker Adam Powell (Pontypridd/Blues Academy) also start against Italy with Bath Rugby centre Tom Cheesman appearing in the national U21 squad for the first time as a replacement.
"We will shortly be selecting the 26 players for the U21 World Cup being staged in France in June and these changes are made with the aim of seeing what sort of strength in depth we have," said Wales U21 Head Coach Chris Davey. "David Flannigan had a couple of appearances for us at last year's World Cup and is a very good player, a lovely passer of the ball who gets his backs moving well.
"However, as a squad we don't feel we have played to our full potential so far and that there is more to come from this team. We have been producing some good stuff but we have not been finishing sides off and we need to be more clinical."
Hook is not the only absentee from the Wales U21 set-up due to the Commonwealth Games - backs coach Dai Rees is also in Australia and his place under Davey is now being filled by WRU National Skills coach Neil Jenkins. The former Wales and Lions fly half, who scored a world record 1,049 Test points, has been shadowing Rees but now steps up a level to join Simon King as an assistant coach.
"Simon is in his second season with us, helping with the forwards, and Neil has been helping with his goal kicking expertise," said Davey. "But, with Dai away in Australia, Neil is now expanding his role with the backs and it is great to have in the environment - he is a legend and the boys love having him around."
Aled Thomas (Newport/Dragons Academy)
Aled Brew (Neath/Ospreys Academy)
Andrew Bishop (Ospreys)
Tom Riley (Pontypridd/Blues Academy)
Chris Czekaj (Cardiff Blues)
David Flannigan (Pontypridd/Blues Academy)
Martin Roberts (Neath/Ospreys Academy)
Rhys Gill (Cardiff/Blues Academy)
Duane Goodfield (Pontypridd/Blues Academy)
Phil Osborne (Newport)
Alun Wyn Jones (Swansea/Ospreys Academy)
Dominic Day (Carmarthen Quins/Scarlets Academy)
Adam Powell (Pontypridd/Blues Academy)
Rhys Shellard (Pontypridd/Blues Academy)
Tom Smith (Neath/Ospreys Academy, captain)
Ed Shervington (Neath)
Craig Mitchell (Neath/Ospreys Academy)
Will Jones (Newport/Dragons Academy)
Ben Lewis (Swansea/Ospreys Academy)
Tom Cheeseman (Bath Rugby)
Liam Davies (Llanelli/Scarlets Academy)
Jamie Roberts (Cardiff/Blues Academy)