| 1 | Microform holoprosencephaly | Enrichment | GLI2, PTCH1, SHH, SUFU | 7.03 |
| 2 | Meningioma | Enrichment | AKT1, SMO, SUFU | 5.36 |
| 3 | Witteveen-kolk syndrome | Enrichment | SIN3A, SIN3B | 5.12 |
| 4 | Postaxial polydactyly type b | Enrichment | GLI1, GLI3 | 5.12 |
| 5 | Polydactyly, postaxial, type a1 | Enrichment | GLI1, GLI3, PTCH1 | 5.04 |
| 6 | Septopreoptic holoprosencephaly | Enrichment | GLI2, PTCH1, SHH | 5.04 |
| 7 | Midline interhemispheric variant of holoprosencephaly | Enrichment | GLI2, PTCH1, SHH | 5.04 |
| 8 | Lobar holoprosencephaly | Enrichment | GLI2, PTCH1, SHH | 4.96 |
| 9 | Alobar holoprosencephaly | Enrichment | GLI2, PTCH1, SHH | 4.87 |
| 10 | Semilobar holoprosencephaly | Enrichment | GLI2, PTCH1, SHH | 4.79 |
| 11 | Polydactyly, preaxial ii | Enrichment | PTCH1, SHH | 4.34 |
| 12 | Basal cell nevus syndrome 1 | Enrichment | PTCH1, SUFU | 3.94 |
| 13 | Combined pituitary hormone deficiency | Enrichment | FOXA2, GLI2 | 3.67 |
| 14 | Ellis-van creveld syndrome | Enrichment | GLI1, PRKACA | 3.57 |
| 15 | Medulloblastoma | Enrichment | PTCH1, SUFU | 3.17 |
| 16 | Macs syndrome | Enrichment | PTCH1, SHH | 2.85 |
| 17 | Craniosynostosis | Enrichment | GLI2, GLI3 | 2.85 |
| 18 | Holoprosencephaly 3 | Enrichment | SHH | 2.55 |
| 19 | Pallister-hall syndrome | Enrichment | GLI3 | 2.55 |
| 20 | Proteus syndrome | Enrichment | AKT1 | 2.55 |
| 21 | Greig cephalopolysyndactyly syndrome | Enrichment | GLI3 | 2.55 |
| 22 | Spermatogenic failure, x-linked, 9 | Enrichment | RBBP7 | 2.55 |
| 23 | Curry-jones syndrome | Enrichment | SMO | 2.55 |
| 24 | Schilbach-rott syndrome | Enrichment | PTCH1 | 2.55 |
| 25 | Polydactyly, preaxial iv | Enrichment | GLI3 | 2.55 |
| 26 | Melorheostosis, isolated | Enrichment | MAP2K1 | 2.55 |
| 27 | Hyperpigmentation with or without hypopigmentation, familial progressive | Enrichment | KITLG | 2.55 |
| 28 | Microphthalmia/coloboma 5 | Enrichment | SHH | 2.55 |
| 29 | Polydactyly, preaxial i | Enrichment | GLI1 | 2.55 |
| 30 | Cardiofaciocutaneous syndrome 3 | Enrichment | MAP2K1 | 2.55 |
| 31 | Culler-jones syndrome | Enrichment | GLI2 | 2.55 |
| 32 | Autoimmune lymphoproliferative syndrome, type iii | Enrichment | PRKCD | 2.55 |
| 33 | Nabais sa-de vries syndrome, type 2 | Enrichment | SPOP | 2.55 |
| 34 | Polydactyly, postaxial, type a8 | Enrichment | GLI1 | 2.55 |
| 35 | Joubert syndrome 32 | Enrichment | SUFU | 2.55 |
| 36 | Neurodevelopmental, jaw, eye, and digital syndrome | Enrichment | FBXW11 | 2.55 |
| 37 | Skin/hair/eye pigmentation, variation in, 7 | Enrichment | KITLG | 2.55 |
| 38 | Melorheostosis | Enrichment | MAP2K1 | 2.55 |
| 39 | Holoprosencephaly 9 | Enrichment | GLI2 | 2.55 |
| 40 | Cowden syndrome 6 | Enrichment | AKT1 | 2.55 |
| 41 | Nabais sa-de vries syndrome, type 1 | Enrichment | SPOP | 2.55 |
| 42 | Pigmented nodular adrenocortical disease, primary, 4 | Enrichment | PRKACA | 2.55 |
| 43 | Cardioacrofacial dysplasia 1 | Enrichment | PRKACA | 2.55 |
| 44 | Intellectual developmental disorder, autosomal dominant 42 | Enrichment | GNB1 | 2.55 |
| 45 | Menke-hennekam syndrome 1 | Enrichment | CREBBP | 2.55 |
| 46 | Ciliary dyskinesia, primary, 46 | Enrichment | STK36 | 2.55 |
| 47 | Deafness, autosomal dominant 69 | Enrichment | KITLG | 2.55 |
| 48 | Rubinstein-taybi syndrome due to 16p13.3 microdeletion | Enrichment | CREBBP | 2.55 |
| 49 | Non-acquired combined pituitary hormone deficiency | Enrichment | FOXA2 | 2.55 |
| 50 | Chromosome 15q24 deletion syndrome | Enrichment | SIN3A | 2.55 |
| 51 | Turner syndrome | Enrichment | PTCH1 | 2.55 |
| 52 | Menke-hennekam syndrome | Enrichment | CREBBP | 2.55 |
| 53 | Familial progressive hyperpigmentation | Enrichment | KITLG | 2.55 |
| 54 | Monosomy 9q22.3 | Enrichment | PTCH1 | 2.55 |
| 55 | Postaxial polydactyly-anterior pituitary anomalies-facial dysmorphism syndrome | Enrichment | GLI2 | 2.55 |
| 56 | Familial progressive hyper- and hypopigmentation | Enrichment | KITLG | 2.55 |
| 57 | Autosomal dominant preaxial polydactyly-upperback hypertrichosis syndrome | Enrichment | SHH | 2.55 |
| 58 | Hirschsprung disease 1 | Enrichment | GLI3, SMO | 2.53 |
| 59 | Pallister-hall-like syndrome | Enrichment | SMO | 2.25 |
| 60 | Thumb deformity | Enrichment | CREBBP | 2.25 |
| 61 | Solitary median maxillary central incisor | Enrichment | SHH | 2.25 |
| 62 | White-sutton syndrome | Enrichment | GLI2 | 2.25 |
| 63 | Bardet-biedl syndrome 22 | Enrichment | IFT172 | 2.25 |
| 64 | Carpenter syndrome 1 | Enrichment | RAB23 | 2.25 |
| 65 | Waardenburg syndrome, type 2f | Enrichment | KITLG | 2.25 |
| 66 | Tibial hemimelia | Enrichment | GLI3 | 2.25 |
| 67 | Acute myeloid leukemia with kat6a-crebbp fusion | Enrichment | CREBBP | 2.25 |
| 68 | Synpolydactyly | Enrichment | GLI3 | 2.25 |
| 69 | Congenital fibrosarcoma | Enrichment | SUFU | 2.25 |
| 70 | Fibrolamellar carcinoma | Enrichment | PRKACA | 2.25 |
| 71 | Basal cell nevus syndrome 2 | Enrichment | SUFU | 2.25 |
| 72 | Primary mediastinal large b-cell lymphoma | Enrichment | XPO1 | 2.25 |
| 73 | Isolated radial hemimelia | Enrichment | SHH | 2.25 |
| 74 | Cerebral visual impairment | Enrichment | GNB1 | 2.25 |
| 75 | Acrocallosal syndrome | Enrichment | GLI3 | 2.08 |
| 76 | Syndactyly, type iv | Enrichment | SHH | 2.08 |
| 77 | Aarskog-scott syndrome | Enrichment | GLI3 | 2.08 |
| 78 | Langerhans cell histiocytosis | Enrichment | MAP2K1 | 2.08 |
| 79 | Holoprosencephaly 7 | Enrichment | PTCH1 | 2.08 |
| 80 | Tethered spinal cord syndrome | Enrichment | CREBBP | 2.08 |
| 81 | Umbilical hernia | Enrichment | GLI3 | 2.08 |
| 82 | Hypoplastic or aplastic tibia with polydactyly | Enrichment | SHH | 2.08 |
| 83 | Intraocular pressure quantitative trait locus | Enrichment | CREBBP | 2.08 |
| 84 | Desmoplastic/nodular medulloblastoma | Enrichment | SUFU | 2.08 |
| 85 | Cardiofaciocutaneous syndrome 1 | Enrichment | MAP2K1 | 1.95 |
| 86 | Schizencephaly | Enrichment | SHH | 1.95 |
| 87 | Short-rib thoracic dysplasia 10 with or without polydactyly | Enrichment | IFT172 | 1.95 |
| 88 | Retinitis pigmentosa 71 | Enrichment | IFT172 | 1.95 |
| 89 | Bardet-biedl syndrome 20 | Enrichment | IFT172 | 1.95 |
| 90 | Cardiofaciocutaneous syndrome | Enrichment | MAP2K1 | 1.95 |
| 91 | Oculomotor apraxia | Enrichment | SUFU | 1.95 |
| 92 | Short-rib thoracic dysplasia 9 with or without polydactyly | Enrichment | IFT172 | 1.86 |
| 93 | Rubinstein-taybi syndrome 1 | Enrichment | CREBBP | 1.78 |
| 94 | Testicular germ cell tumor | Enrichment | KITLG | 1.78 |
| 95 | Chromosome 16p13.3 deletion syndrome, proximal | Enrichment | CREBBP | 1.78 |
| 96 | Basal cell carcinoma 1 | Enrichment | PTCH1 | 1.78 |
| 97 | Breast adenocarcinoma | Enrichment | AKT1 | 1.78 |
| 98 | Hypertrichosis | Enrichment | CREBBP | 1.78 |
| 99 | Autism | Enrichment | CREBBP, SHH | 1.76 |
| 100 | Waardenburg syndrome, type 2e | Enrichment | KITLG | 1.71 |
| 101 | Capillary malformation-arteriovenous malformation 1 | Enrichment | MAP2K1 | 1.71 |
| 102 | Congenital hydrocephalus | Enrichment | PTCH1 | 1.71 |
| 103 | Overgrowth syndrome | Enrichment | PTCH1 | 1.71 |
| 104 | Hypothyroidism | Enrichment | GNB1 | 1.65 |
| 105 | Isolated split hand-split foot malformation | Enrichment | BTRC | 1.65 |
| 106 | Arteriovenous malformation | Enrichment | MAP2K1 | 1.60 |
| 107 | Cowden syndrome | Enrichment | AKT1 | 1.60 |
| 108 | Myopathy, x-linked, with excessive autophagy | Enrichment | MAP2K1 | 1.56 |
| 109 | Meningioma, familial | Enrichment | SUFU | 1.52 |
| 110 | Leukemia, acute lymphoblastic | Enrichment | GNB1 | 1.52 |
| 111 | Myelodysplastic syndrome | Enrichment | GNB1 | 1.52 |
| 112 | Lung non-small cell carcinoma | Enrichment | MAP2K1 | 1.52 |
| 113 | Ovarian cancer | Enrichment | AKT1, PTCH1 | 1.49 |
| 114 | Septooptic dysplasia | Enrichment | SHH | 1.48 |
| 115 | Short-rib thoracic dysplasia 6 with or without polydactyly | Enrichment | IFT172 | 1.48 |
| 116 | Diaphragmatic hernia, congenital | Enrichment | GLI3 | 1.45 |
| 117 | Autism spectrum disorder | Enrichment | GNB1, MAP2K1 | 1.43 |
| 118 | Heart disease | Enrichment | CREBBP | 1.41 |
| 119 | Corpus callosum, agenesis of | Enrichment | CREBBP | 1.38 |
| 120 | Isolated corpus callosum agenesis | Enrichment | CREBBP | 1.38 |
| 121 | Rare genetic intellectual disability | Enrichment | CREBBP | 1.38 |
| 122 | Intellectual disability-hypoplastic corpus callosum-preauricular tag syndrome | Enrichment | CREBBP | 1.38 |
| 123 | Noonan syndrome and noonan-related syndrome | Enrichment | MAP2K1 | 1.38 |
| 124 | Rhabdomyosarcoma | Enrichment | PTCH1 | 1.36 |
| 125 | Cleft palate, isolated | Enrichment | GNB1 | 1.33 |
| 126 | Diffuse large b-cell lymphoma | Enrichment | CREBBP | 1.28 |
| 127 | Inherited cancer-predisposing syndrome | Enrichment | PTCH1, SUFU | 1.28 |
| 128 | Microphthalmia | Enrichment | PTCH1 | 1.22 |
| 129 | Noonan syndrome 1 | Enrichment | MAP2K1 | 1.20 |
| 130 | Scoliosis | Enrichment | CREBBP | 1.19 |
| 131 | Rasopathy | Enrichment | MAP2K1 | 1.15 |
| 132 | Strabismus | Enrichment | GNB1 | 1.14 |
| 133 | Isolated joubert syndrome | Enrichment | SUFU | 1.09 |
| 134 | Short-rib thoracic dysplasia 1 with or without polydactyly | Enrichment | IFT172 | 1.05 |
| 135 | Nephronophthisis | Enrichment | PIAS1 | 1.05 |
| 136 | Dystonia | Enrichment | GNB1 | 1.03 |
| 137 | Cerebral palsy | Enrichment | GNB1 | 0.98 |
| 138 | Bardet-biedl syndrome | Enrichment | IFT172 | 0.95 |
| 139 | Hereditary breast carcinoma | Enrichment | AKT1 | 0.93 |
| 140 | Retinitis pigmentosa | Enrichment | IFT172, IFT88 | 0.93 |
| 141 | Joubert syndrome 1 | Enrichment | IFT172 | 0.88 |
| 142 | Autosomal dominant non-syndromic intellectual disability | Enrichment | GNB1 | 0.88 |
| 143 | Rare autosomal dominant non-syndromic sensorineural deafness type dfna | Enrichment | KITLG | 0.87 |
| 144 | Hereditary breast ovarian cancer syndrome | Enrichment | PTCH1 | 0.84 |
| 145 | Myeloma, multiple | Enrichment | CREBBP | 0.84 |
| 146 | Male infertility with azoospermia or oligozoospermia due to single gene mutation | Enrichment | GLI2 | 0.84 |
| 147 | Breast cancer | Enrichment | AKT1 | 0.72 |
| 148 | Primary ciliary dyskinesia | Enrichment | STK36 | 0.72 |
| 149 | Colorectal cancer | Enrichment | AKT1 | 0.66 |
| 150 | Congenital nervous system abnormality | Enrichment | CREBBP | 0.59 |
| 151 | Nervous system disease | Enrichment | CREBBP | 0.59 |
| 152 | Microcephaly | Enrichment | GNB1 | 0.53 |
| 153 | Complex neurodevelopmental disorder | Enrichment | FBXW11 | 0.53 |
| 154 | Hereditary retinal dystrophy | Enrichment | IFT172 | 0.25 |
| 155 | Fundus dystrophy | Enrichment | IFT172 | 0.25 |