Table 4 The most different phenotype pairs within multi-phenotype disease genes by the mLOF score

Facioscapulohumeral muscular dystrophy 2

Bosma Arhinia Microphthalmia Syndrome

Cardiofaciocutaneous syndrome 2

Multiple myeloma

Rapp-Hodgkin syndrome

Split-Hand/foot malformation 4

Retinitis pigmentosa

Retinitis pigmentosa 13

Schwannomatosis

Coffin-Siris syndrome 3

Pseudopseudohypoparathyroidism

Pituitary adenoma 3, multiple types, somatic

Noonan syndrome 1

Multiple myeloma

Cholestasis, progressive familial intrahepatic 2

Cholestasis, intrahepatic, of pregnancy 3

Long QT syndrome 9

Rippling muscle disease

Renal cell carcinoma, papillary, 1, familial and somatic

CEBALID syndrome

Dyskinesia with orofacial involvement, autosomal recessive

Dyskinesia, familial, with facial myokymia

Epileptic encephalopathy, early infantile, 29

Charcot-Marie-Tooth disease, axonal, type 2 N

Tooth agenesis, selective, 7

Coronary artery disease, autosomal dominant 2

Deafness, X-linked 5

Spondyloepimetaphyseal dysplasia, X-linked, with mental deterioration

Mental retardation, X-linked, with or without seizures, ARX-related

Corpus callosum, agenesis of, with abnormal genitalia

Hypergonadotropic hypogonadism

Precocious puberty, male

Perrault syndrome 5

Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 3

Congenital myopathy 2B, severe infantile, autosomal recessive

Congenital myopathy 2 C, severe infantile, autosomal dominant

Breast cancer

Medulloblastoma

Macular dystrophy, vitelliform, 5

Macular dystrophy, vitelliform, 2

Heinz body anemias

Methemoglobinemia, Alpha type

Generalised epilepsy with febrile seizures plus, type 12

Developmental and epileptic encephalopathy 114

Congenital myopathy 22 A, classic

Paramyotonia congenita

Exostoses, multiple, type II

Ovarian cancer

RAPADILINO syndrome

Ovarian cancer

Leukodystrophy, hypomyelinating, 8, with or without oligodontia and/or hypogonadotropic hypogonadism

Charcot-Marie-Tooth disease, demyelinating, type 1I

Lipoprotein glomerulopathy

Hyperlipoproteinemia, type III

Acromesomelic dysplasia, Maroteaux type

Short stature with nonspecific skeletal abnormalities

Gerstmann-Straussler disease

Creutzfeldt-Jakob disease

Cardiac valvular dysplasia, X-linked

Otopalatodigital syndrome, type I

Cardiomyopathy, dilated, 1 G

Myopathy, myofibrillar, 9, with early respiratory failure

Mitochondrial complex II deficiency, nuclear type 3

Pheochromocytoma

Bestrophinopathy, autosomal recessive

Vitreoretinochoroidopathy

Rett syndrome

Mental retardation, X-linked, syndromic 13

Hypothyroidism, congenital, nongoitrous, 1

Ovarian cancer

Metatropic dysplasia

Hereditary motor and sensory neuropathy, type IIC