class Patient(Base):
    __tablename__ = 'patients'
    id = Column(Integer, primary_key=True, nullable=False)
    mother_id = Column(Integer, ForeignKey('patients.id'), index=True)
    mother = relationship('Patient', primaryjoin='Patient.id==Patient.mother_id', remote_side='Patient.id', uselist=False)
    phenoscore = Column(Float)

patients = Patient.query.filter(Patient.mother.phenoscore == 10)

patients = Patient.query.filter(Patient.mother.has(phenoscore=10))

patients = Patient.query.join(Patient.mother, aliased=True)
                    .filter_by(phenoscore=10)

Patient.where(mother___phenoscore=10)

Comment.where(post___public=True, post___user___name__like='Bi%')

db_session.query(Patient).join(Patient.mother)
    .filter(Patient.mother.property.mapper.class_.phenoscore==10)

Patient.query.join(Patient.mother)
    .filter(Patient.mother.property.mapper.class_.phenoscore==10)