| 1 | Combined pituitary hormone deficiency | Enrichment | FOXA2, GLI2, OTX2 | 6.27 |
| 2 | Septooptic dysplasia | Enrichment | OTX2, SHH, SOX2 | 5.67 |
| 3 | Septopreoptic holoprosencephaly | Enrichment | FGF8, GLI2, SHH | 5.36 |
| 4 | Midline interhemispheric variant of holoprosencephaly | Enrichment | FGF8, GLI2, SHH | 5.36 |
| 5 | Microform holoprosencephaly | Enrichment | FGF8, GLI2, SHH | 5.27 |
| 6 | Lobar holoprosencephaly | Enrichment | FGF8, GLI2, SHH | 5.27 |
| 7 | Alobar holoprosencephaly | Enrichment | FGF8, GLI2, SHH | 5.19 |
| 8 | Semilobar holoprosencephaly | Enrichment | FGF8, GLI2, SHH | 5.11 |
| 9 | Macs syndrome | Enrichment | OTX2, SHH, SOX2 | 4.96 |
| 10 | Haddad syndrome | Enrichment | ASCL1, RET | 4.55 |
| 11 | Nanophthalmos | Enrichment | OTX2, SOX2 | 3.59 |
| 12 | Microphthalmia | Enrichment | OTX2, SOX2 | 2.97 |
| 13 | Holoprosencephaly 3 | Enrichment | SHH | 2.66 |
| 14 | Multiple endocrine neoplasia, type iib | Enrichment | RET | 2.66 |
| 15 | Focal segmental glomerulosclerosis 10 | Enrichment | LMX1B | 2.66 |
| 16 | Maturity-onset diabetes of the young, type 6 | Enrichment | NEUROD1 | 2.66 |
| 17 | Nail-patella syndrome | Enrichment | LMX1B | 2.66 |
| 18 | Microphthalmia/coloboma 5 | Enrichment | SHH | 2.66 |
| 19 | Polydactyly, preaxial i | Enrichment | GLI1 | 2.66 |
| 20 | Culler-jones syndrome | Enrichment | GLI2 | 2.66 |
| 21 | Endove syndrome, limb-brain type | Enrichment | EN1 | 2.66 |
| 22 | Polydactyly, postaxial, type a8 | Enrichment | GLI1 | 2.66 |
| 23 | T-cell large granular lymphocyte leukemia | Enrichment | STAT3 | 2.66 |
| 24 | Microphthalmia, syndromic 5 | Enrichment | OTX2 | 2.66 |
| 25 | Bone mineral density quantitative trait locus 16 | Enrichment | WNT1 | 2.66 |
| 26 | Parkinsonism-dystonia 1, infantile-onset | Enrichment | SLC6A3 | 2.66 |
| 27 | Holoprosencephaly 9 | Enrichment | GLI2 | 2.66 |
| 28 | Pituitary hormone deficiency, combined, 6 | Enrichment | OTX2 | 2.66 |
| 29 | Hypogonadotropic hypogonadism 6 with or without anosmia | Enrichment | FGF8 | 2.66 |
| 30 | Autoimmune disease, multisystem, infantile-onset, 1 | Enrichment | STAT3 | 2.66 |
| 31 | Lipoid nephrosis | Enrichment | LMX1B | 2.66 |
| 32 | Intellectual developmental disorder with language impairment and early-onset dopa-responsive dystonia-parkinsonism | Enrichment | NR4A2 | 2.66 |
| 33 | Classic dopamine transporter deficiency syndrome | Enrichment | SLC6A3 | 2.66 |
| 34 | Non-acquired combined pituitary hormone deficiency | Enrichment | FOXA2 | 2.66 |
| 35 | Stat3-related early-onset multisystem autoimmune disease | Enrichment | STAT3 | 2.66 |
| 36 | Thyroid cancer | Enrichment | RET | 2.66 |
| 37 | Congenital cataract-anterior segment dysgenesis syndrome | Enrichment | PITX3 | 2.66 |
| 38 | Intrauterine growth restriction-short stature-early adult-onset diabetes syndrome | Enrichment | CDKN1C | 2.66 |
| 39 | Parkinsonism-dystonia, infantile | Enrichment | SLC6A3 | 2.66 |
| 40 | Postaxial polydactyly-anterior pituitary anomalies-facial dysmorphism syndrome | Enrichment | GLI2 | 2.66 |
| 41 | Chronic lymphoproliferative disorder of natural killer cells | Enrichment | STAT3 | 2.66 |
| 42 | Gastrointestinal system disease | Enrichment | RET | 2.66 |
| 43 | Autosomal dominant preaxial polydactyly-upperback hypertrichosis syndrome | Enrichment | SHH | 2.66 |
| 44 | Multiple endocrine neoplasia | Enrichment | RET | 2.66 |
| 45 | Camurati-engelmann disease 1 | Enrichment | TGFB1 | 2.35 |
| 46 | Agnathia-otocephaly complex | Enrichment | OTX2 | 2.35 |
| 47 | Cataract 11, multiple types | Enrichment | PITX3 | 2.35 |
| 48 | Anterior segment dysgenesis 1 | Enrichment | PITX3 | 2.35 |
| 49 | Segawa syndrome, autosomal recessive | Enrichment | TH | 2.35 |
| 50 | Osteogenesis imperfecta, type xv | Enrichment | WNT1 | 2.35 |
| 51 | Solitary median maxillary central incisor | Enrichment | SHH | 2.35 |
| 52 | Orofacial cleft 5 | Enrichment | MSX1 | 2.35 |
| 53 | Intrauterine growth retardation, metaphyseal dysplasia, adrenal hypoplasia congenita, and genital anomalies | Enrichment | CDKN1C | 2.35 |
| 54 | White-sutton syndrome | Enrichment | GLI2 | 2.35 |
| 55 | Witkop syndrome | Enrichment | MSX1 | 2.35 |
| 56 | Aromatic l-amino acid decarboxylase deficiency | Enrichment | DDC | 2.35 |
| 57 | Parkinsonism-dystonia 2, infantile-onset | Enrichment | SLC18A2 | 2.35 |
| 58 | Inflammatory bowel disease, immunodeficiency, and encephalopathy | Enrichment | TGFB1 | 2.35 |
| 59 | Camurati-engelmann disease | Enrichment | TGFB1 | 2.35 |
| 60 | Deafness, autosomal dominant 7 | Enrichment | LMX1A | 2.35 |
| 61 | Medullary thyroid carcinoma | Enrichment | RET | 2.35 |
| 62 | 9q33.3q34.11 microdeletion syndrome | Enrichment | LMX1B | 2.35 |
| 63 | Postaxial polydactyly type b | Enrichment | GLI1 | 2.35 |
| 64 | Developmental delay-language impairment-dopa responsive dystonia-parkinsonism syndrome due to 2q24 microdeletion | Enrichment | NR4A2 | 2.35 |
| 65 | Isolated radial hemimelia | Enrichment | SHH | 2.35 |
| 66 | Sensorineural hearing loss | Enrichment | LMX1A, RET | 2.30 |
| 67 | Hyper-ige syndrome 1, autosomal dominant, with recurrent infections | Enrichment | STAT3 | 2.18 |
| 68 | Dystonia, dopa-responsive | Enrichment | TH | 2.18 |
| 69 | Thyroid carcinoma, familial medullary | Enrichment | RET | 2.18 |
| 70 | Syndactyly, type iv | Enrichment | SHH | 2.18 |
| 71 | Osteoporosis, juvenile | Enrichment | WNT1 | 2.18 |
| 72 | Breast implant-associated anaplastic large cell lymphoma | Enrichment | STAT3 | 2.18 |
| 73 | Hyper ige syndrome | Enrichment | STAT3 | 2.18 |
| 74 | Gingival overgrowth | Enrichment | RET | 2.18 |
| 75 | Hypoplastic or aplastic tibia with polydactyly | Enrichment | SHH | 2.18 |
| 76 | Gtp cyclohydrolase 1-deficient dopa-responsive dystonia | Enrichment | NR4A2 | 2.18 |
| 77 | Butterfly-shaped pigment dystrophy | Enrichment | OTX2 | 2.18 |
| 78 | Male infertility with azoospermia or oligozoospermia due to single gene mutation | Enrichment | FGF8, GLI2 | 2.17 |
| 79 | Polydactyly, preaxial ii | Enrichment | SHH | 2.05 |
| 80 | Microphthalmia, syndromic 3 | Enrichment | SOX2 | 2.05 |
| 81 | Schizencephaly | Enrichment | SHH | 2.05 |
| 82 | Developmental and epileptic encephalopathy 4 | Enrichment | LMX1B | 2.05 |
| 83 | Tobacco addiction | Enrichment | SLC6A3 | 2.05 |
| 84 | Central hypoventilation syndrome, congenital, 1 | Enrichment | RET | 2.05 |
| 85 | Silver-russell syndrome due to a point mutation | Enrichment | CDKN1C | 2.05 |
| 86 | Cleft lip and alveolus | Enrichment | MSX1 | 2.05 |
| 87 | Multiple endocrine neoplasia, type iia | Enrichment | RET | 1.96 |
| 88 | Holoprosencephaly | Enrichment | FGF8 | 1.96 |
| 89 | Cleft upper lip | Enrichment | MSX1 | 1.96 |
| 90 | Holoprosencephaly 1 | Enrichment | FGF8 | 1.88 |
| 91 | Anxiety | Enrichment | OTX2 | 1.88 |
| 92 | Inflammatory bowel disease 25, autosomal recessive | Enrichment | TGFB1 | 1.88 |
| 93 | Il10-related early-onset inflammatory bowel disease | Enrichment | TGFB1 | 1.88 |
| 94 | Sporadic pheochromocytoma/secreting paraganglioma | Enrichment | RET | 1.88 |
| 95 | Renal hypodysplasia/aplasia 1 | Enrichment | RET | 1.76 |
| 96 | Hypothyroidism | Enrichment | RET | 1.76 |
| 97 | Permanent neonatal diabetes mellitus | Enrichment | STAT3 | 1.76 |
| 98 | Early-onset posterior polar cataract | Enrichment | PITX3 | 1.76 |
| 99 | Tooth agenesis, selective, 1 | Enrichment | MSX1 | 1.70 |
| 100 | Ellis-van creveld syndrome | Enrichment | GLI1 | 1.70 |
| 101 | Congenital central hypoventilation syndrome | Enrichment | RET | 1.70 |
| 102 | Renal agenesis, bilateral | Enrichment | RET | 1.70 |
| 103 | Renal hypodysplasia/aplasia 3 | Enrichment | RET | 1.58 |
| 104 | Osteogenesis imperfecta, type iv | Enrichment | WNT1 | 1.55 |
| 105 | Acute promyelocytic leukemia | Enrichment | STAT3 | 1.55 |
| 106 | Osteoporosis | Enrichment | WNT1 | 1.52 |
| 107 | Pheochromocytoma | Enrichment | RET | 1.52 |
| 108 | Cleft lip/palate | Enrichment | MSX1 | 1.52 |
| 109 | 46,xy partial gonadal dysgenesis | Enrichment | OTX2 | 1.52 |
| 110 | Polydactyly, postaxial, type a1 | Enrichment | GLI1 | 1.49 |
| 111 | Osteogenesis imperfecta, type iii | Enrichment | WNT1 | 1.49 |
| 112 | Beckwith-wiedemann syndrome | Enrichment | CDKN1C | 1.41 |
| 113 | Normosmic congenital hypogonadotropic hypogonadism | Enrichment | FGF8 | 1.41 |
| 114 | Diffuse large b-cell lymphoma | Enrichment | STAT3 | 1.38 |
| 115 | Parkinson's disease | Enrichment | NR4A2 | 1.38 |
| 116 | Williams-beuren syndrome | Enrichment | CDKN1C | 1.36 |
| 117 | Maturity-onset diabetes of the young | Enrichment | NEUROD1 | 1.36 |
| 118 | Craniosynostosis | Enrichment | GLI2 | 1.36 |
| 119 | Hereditary paraganglioma-pheochromocytoma syndromes | Enrichment | RET | 1.34 |
| 120 | Hepatocellular carcinoma | Enrichment | RET | 1.32 |
| 121 | Tooth agenesis | Enrichment | MSX1 | 1.32 |
| 122 | Brittle bone disorder | Enrichment | WNT1 | 1.30 |
| 123 | Kallmann syndrome | Enrichment | FGF8 | 1.30 |
| 124 | Parkinson disease, late-onset | Enrichment | NR4A2 | 1.29 |
| 125 | Tetralogy of fallot | Enrichment | RET | 1.25 |
| 126 | Rasopathy | Enrichment | DDC | 1.25 |
| 127 | Hirschsprung disease 1 | Enrichment | RET | 1.21 |
| 128 | Differentiated thyroid carcinoma | Enrichment | RET | 1.21 |
| 129 | Cystic fibrosis | Enrichment | TGFB1 | 1.16 |
| 130 | Dystonia | Enrichment | TH | 1.13 |
| 131 | Epilepsy | Enrichment | NR4A2 | 1.07 |
| 132 | Type 2 diabetes mellitus | Enrichment | NEUROD1 | 1.05 |
| 133 | Nephrotic syndrome | Enrichment | LMX1B | 1.04 |
| 134 | Hereditary breast carcinoma | Enrichment | RET | 1.03 |
| 135 | Hypertelorism | Enrichment | RET | 0.96 |
| 136 | Autism | Enrichment | SHH | 0.83 |
| 137 | Breast cancer | Enrichment | RET | 0.81 |
| 138 | Colorectal cancer | Enrichment | RET | 0.76 |
| 139 | Leber plus disease | Enrichment | OTX2 | 0.72 |
| 140 | Ovarian cancer | Enrichment | RET | 0.70 |
| 141 | Autism spectrum disorder | Enrichment | NR4A2 | 0.67 |
| 142 | Complex neurodevelopmental disorder | Enrichment | NR4A2 | 0.62 |
| 143 | Inherited cancer-predisposing syndrome | Enrichment | RET | 0.59 |
| 144 | Hereditary retinal dystrophy | Enrichment | NEUROD1 | 0.32 |
| 145 | Fundus dystrophy | Enrichment | NEUROD1 | 0.32 |