Example:
‘Lutembacher’s syndrome’ is-a ‘Congenital atrial septal defect’
‘Lutembacher’s syndrome is-a ‘Congenital stenosis of mitral valve’

This disease is a combined malformation of the heart. The septal defect and the stenosis are parts of this syndrome.
(therefore the correct axiom would be
‘Lutembacher’s syndrome’ is-a (has-part some ‘Congenital atrial septal defect’ ) and (has-part some ‘Congenital stenosis of mitral valve’ )

I interpret the use of is-a in this (and many similar other cases) that what is meant is the following:
‘Patient with Lutembacher’s syndrome’ is-a ‘Patient with Congenital atrial septal defect’
‘Patient with Lutembacher’s syndrome is-a ‘Patient with Congenital stenosis of mitral valve’

The problem is that disease concepts are not interpreted as representing pathological structures or dispositions but as representing their bearers.