1. much depends on from what source was the consideration paid for purchase of the flat
2. was the consideration paid out of joint family funds or the exclusive funds of the mother and son?
3. if the flat was purchased using the funds of mother and son then it becomes their self acquired property
4. if the flat was purchased out of joint family funds then it becomes a HUF property
5. assuming the flat is self acquired, then on mother's demise, her half share will devolve on her husband and children [equally] - see section 15 of Hindu Succession Act
6. mere transfer of share certificate in the exclusive name of son does not confer full ownership rights in the flat in favour of son. Share certificate is not even a title document!
7. so the sisters can claim their share through the mother
8. assuming the property is HUF property then since the father was alive on 9.9.2005 [when the Hindu Succession Amendment act was passed giving daughters equal rights in HUF property], then sisters can claim as coparcenors.
9. whatever may be the holding - self acquired or ancestral - just because the share certificate stands in the sole name of the son - he does not become absolute owner of the flat - the sisters can nonetheless claim either through the mother [in case flat is self acquired] or as coparcenors [in case flat is HUF property]