My son has lived with his partner for 3 years and they have a two year old son. The house they live in is mortgaged in my son and his previous partners name, which was taken out 5 years ago. His previous partner has never contributed to the mortgage and my son could not remove her name as the mortgage company said that he could not do a transfer of equity as he did not earn enough to take the mortgage in sole name. His new partner had a lot of debt so was unable to be put on the mortgage. The debts have now been repaid. He has arrived home tonight from work and is devastated to find the house stripped of furniture and his partner and son gone. He has attempted to contact his partner to be told that she can only speak to him through a solicitor. So what I need to know is , what rights does he have as a father to see his son and can his new partner try to take his house from him because they have a child together?

You need to say where you live, and if he is on the birth certificate.
She cannot take the house, from what you have said here.
(The ex who is on the mortgage, if she is also on the deed, has the same rights he has to half the house, regardless of whether she paid a dime or not. You need to find out if she is on the deed.)

As joy noted, she cannot take the house. Taking the furniture, unless there is proof that she helped pay for the furniture, may have been illegal.

Since you referred to a solicitor, I assume you are in the UK, but ANY question on law needs to include your general locale as laws vary by area.

Your son needs to consult a solicitor ASAP. If there were any belongings removed from the house that the new partner doesn't own (anything that was in the house when the partner moved in), then he may be able to swear out a warrant for theft.

As for the child, he has equal rights to the child. However, if he isn't listed on the birth certificate, he will have to go to court to establish paternity and custody. In either case, he will have to go to court to establish joint legal custody and to have a visitation schedule setup.

You refer to the partner's debts. Did you son help payoff those debts? Can he prove it? If so, the partner leaving after the debts were paid may be suspicious.

But since the partner has a solicitor, then your son NEEDS one too. If he has been informed to only contact the partner through her solicitor, then he has to abide by that. But that doesn't mean he can't take action. But he needs his own solicitor to know what action he can take according to local law.