| 1 | 46,xy complete gonadal dysgenesis | Direct | | |
| 2 | Alobar holoprosencephaly | Enrichment | CDON, DISP1, GAS1, GLI2, PTCH1, SHH, STIL | 10.74 |
| 3 | Semilobar holoprosencephaly | Enrichment | CDON, DISP1, GAS1, GLI2, PTCH1, SHH, STIL | 10.67 |
| 4 | Septopreoptic holoprosencephaly | Enrichment | CDON, DISP1, GAS1, GLI2, PTCH1, SHH, STIL | 10.38 |
| 5 | Midline interhemispheric variant of holoprosencephaly | Enrichment | CDON, DISP1, GAS1, GLI2, PTCH1, SHH, STIL | 10.38 |
| 6 | Lobar holoprosencephaly | Enrichment | CDON, DISP1, GAS1, GLI2, PTCH1, SHH, STIL | 10.33 |
| 7 | Microform holoprosencephaly | Enrichment | CDON, DISP1, GAS1, GLI2, PTCH1, SHH | 10.33 |
| 8 | Meningioma | Enrichment | AKT1, PIK3CA, SMO | 5.97 |
| 9 | Polydactyly, preaxial ii | Enrichment | PTCH1, SHH | 5.74 |
| 10 | Congenital lipomatous overgrowth, vascular malformations, and epidermal nevi | Enrichment | PIK3CA, PIK3R1 | 5.05 |
| 11 | Hirschsprung disease 1 | Enrichment | GLI3, IHH, SMO | 4.76 |
| 12 | Basal cell nevus syndrome 1 | Enrichment | PTCH1, PTCH2 | 4.35 |
| 13 | Basal cell carcinoma 1 | Enrichment | PTCH1, PTCH2 | 4.35 |
| 14 | Breast adenocarcinoma | Enrichment | AKT1, PIK3CA | 4.35 |
| 15 | Macs syndrome | Enrichment | PTCH1, SHH | 4.24 |
| 16 | Overgrowth syndrome | Enrichment | PIK3R1, PTCH1 | 4.20 |
| 17 | Cowden syndrome | Enrichment | AKT1, PIK3CA | 3.97 |
| 18 | Medulloblastoma | Enrichment | PTCH1, PTCH2 | 3.57 |
| 19 | Breast cancer | Enrichment | AKT1, PIK3CA, PTCH2 | 3.52 |
| 20 | Polydactyly, postaxial, type a1 | Enrichment | GLI3, PTCH1 | 3.51 |
| 21 | Colorectal cancer | Enrichment | AKT1, PIK3CA, PIK3R1 | 3.33 |
| 22 | Craniosynostosis | Enrichment | GLI2, GLI3 | 3.25 |
| 23 | Holoprosencephaly 3 | Enrichment | SHH | 3.23 |
| 24 | 46,xy sex reversal 7 | Enrichment | DHH | 3.23 |
| 25 | Schilbach-rott syndrome | Enrichment | PTCH1 | 3.23 |
| 26 | Microphthalmia/coloboma 5 | Enrichment | SHH | 3.23 |
| 27 | Acrocapitofemoral dysplasia | Enrichment | IHH | 3.23 |
| 28 | Holoprosencephaly 11 | Enrichment | CDON | 3.23 |
| 29 | Turner syndrome | Enrichment | PTCH1 | 3.23 |
| 30 | Monosomy 9q22.3 | Enrichment | PTCH1 | 3.23 |
| 31 | Autosomal dominant preaxial polydactyly-upperback hypertrichosis syndrome | Enrichment | SHH | 3.23 |
| 32 | Ovarian cancer | Enrichment | AKT1, PIK3CA, PTCH1 | 3.14 |
| 33 | 46,xy gonadal dysgenesis with minifascicular neuropathy | Enrichment | DHH | 2.93 |
| 34 | Solitary median maxillary central incisor | Enrichment | SHH | 2.93 |
| 35 | Isolated radial hemimelia | Enrichment | SHH | 2.93 |
| 36 | Brachydactyly, type a1 | Enrichment | IHH | 2.75 |
| 37 | Syndactyly, type iv | Enrichment | SHH | 2.75 |
| 38 | Holoprosencephaly 7 | Enrichment | PTCH1 | 2.75 |
| 39 | Hypoplastic or aplastic tibia with polydactyly | Enrichment | SHH | 2.75 |
| 40 | Pallister-hall syndrome | Enrichment | GLI3 | 2.75 |
| 41 | Macrodactyly | Enrichment | PIK3CA | 2.75 |
| 42 | Proteus syndrome | Enrichment | AKT1 | 2.75 |
| 43 | Greig cephalopolysyndactyly syndrome | Enrichment | GLI3 | 2.75 |
| 44 | Curry-jones syndrome | Enrichment | SMO | 2.75 |
| 45 | Polydactyly, preaxial iv | Enrichment | GLI3 | 2.75 |
| 46 | Megalencephaly, autosomal dominant | Enrichment | PIK3CA | 2.75 |
| 47 | Cowden syndrome 5 | Enrichment | PIK3CA | 2.75 |
| 48 | Donnai-barrow syndrome | Enrichment | LRP2 | 2.75 |
| 49 | Culler-jones syndrome | Enrichment | GLI2 | 2.75 |
| 50 | Microcephaly 7, primary, autosomal recessive | Enrichment | STIL | 2.75 |
| 51 | Cerebral cavernous malformations 4 | Enrichment | PIK3CA | 2.75 |
| 52 | Short syndrome | Enrichment | PIK3R1 | 2.75 |
| 53 | Nivelon-nivelon-mabille syndrome | Enrichment | HHAT | 2.75 |
| 54 | Camurati-engelmann disease 2 | Enrichment | TGFB2 | 2.75 |
| 55 | Hemifacial myohyperplasia | Enrichment | PIK3CA | 2.75 |
| 56 | Capillary malformation of the lower lip, lymphatic malformation of face and neck, asymmetry of face and limbs, and partial/generalized overgrowth | Enrichment | PIK3CA | 2.75 |
| 57 | Holoprosencephaly 9 | Enrichment | GLI2 | 2.75 |
| 58 | Immunodeficiency 36 with lymphoproliferation | Enrichment | PIK3R1 | 2.75 |
| 59 | Cowden syndrome 6 | Enrichment | AKT1 | 2.75 |
| 60 | Brachydactyly, type e2 | Enrichment | PTHLH | 2.75 |
| 61 | Agammaglobulinemia 7, autosomal recessive | Enrichment | PIK3R1 | 2.75 |
| 62 | Holoprosencephaly 10 | Enrichment | DISP1 | 2.75 |
| 63 | Segmental progressive overgrowth syndrome with fibroadipose hyperplasia | Enrichment | PIK3CA | 2.75 |
| 64 | Prolactin-producing pituitary gland adenoma | Enrichment | LRP2 | 2.75 |
| 65 | Hypospadias | Enrichment | PIK3CA | 2.75 |
| 66 | Rare venous malformation | Enrichment | PIK3CA | 2.75 |
| 67 | Diaphragmatic eventration | Enrichment | PIK3CA | 2.75 |
| 68 | Pik3ca-related overgrowth spectrum | Enrichment | PIK3CA | 2.75 |
| 69 | Rare combined vascular malformation | Enrichment | PIK3CA | 2.75 |
| 70 | Cavernous lymphangioma | Enrichment | PIK3CA | 2.75 |
| 71 | Pik3ca-related overgrowth syndrome | Enrichment | PIK3CA | 2.75 |
| 72 | Postaxial polydactyly-anterior pituitary anomalies-facial dysmorphism syndrome | Enrichment | GLI2 | 2.75 |
| 73 | Hemihyperplasia-multiple lipomatosis syndrome | Enrichment | PIK3CA | 2.75 |
| 74 | Eccrine angiomatous hamartoma | Enrichment | PIK3CA | 2.75 |
| 75 | Macrodactyly of toe | Enrichment | PIK3CA | 2.75 |
| 76 | Schizencephaly | Enrichment | SHH | 2.63 |
| 77 | Hereditary breast carcinoma | Enrichment | AKT1, PIK3CA | 2.57 |
| 78 | Pallister-hall-like syndrome | Enrichment | SMO | 2.45 |
| 79 | Keratosis, seborrheic | Enrichment | PIK3CA | 2.45 |
| 80 | White-sutton syndrome | Enrichment | GLI2 | 2.45 |
| 81 | Noonan syndrome 8 | Enrichment | PIK3CA | 2.45 |
| 82 | Tibial hemimelia | Enrichment | GLI3 | 2.45 |
| 83 | Rosette-forming glioneuronal tumor | Enrichment | PIK3CA | 2.45 |
| 84 | Synpolydactyly | Enrichment | GLI3 | 2.45 |
| 85 | Loeys-dietz syndrome 4 | Enrichment | TGFB2 | 2.45 |
| 86 | Postaxial polydactyly type b | Enrichment | GLI3 | 2.45 |
| 87 | Non-syndromic syndactyly | Enrichment | LRP2 | 2.45 |
| 88 | Commissural facial cleft | Enrichment | PTCH2 | 2.45 |
| 89 | Congenital hydrocephalus | Enrichment | PTCH1 | 2.38 |
| 90 | Brachydactyly, type e1 | Enrichment | PTHLH | 2.28 |
| 91 | Acrocallosal syndrome | Enrichment | GLI3 | 2.28 |
| 92 | Pompe disease, infantile-onset | Enrichment | PIK3CA | 2.28 |
| 93 | Aarskog-scott syndrome | Enrichment | GLI3 | 2.28 |
| 94 | Immunodeficiency 14a with lymphoproliferation, autosomal dominant | Enrichment | PIK3R1 | 2.28 |
| 95 | Umbilical hernia | Enrichment | GLI3 | 2.28 |
| 96 | Myopia 23, autosomal recessive | Enrichment | LRPAP1 | 2.28 |
| 97 | Immunodeficiency 14 | Enrichment | PIK3R1 | 2.28 |
| 98 | Keratoacanthoma | Enrichment | PIK3CA | 2.28 |
| 99 | Septooptic dysplasia | Enrichment | SHH | 2.15 |
| 100 | Megalencephaly-capillary malformation-polymicrogyria syndrome | Enrichment | PIK3CA | 2.15 |
| 101 | Cerebrovascular disease | Enrichment | PIK3CA | 2.15 |
| 102 | Prolactinoma | Enrichment | LRP2 | 2.15 |
| 103 | Familial cerebral cavernous malformations | Enrichment | PIK3CA | 2.15 |
| 104 | Microphthalmia/coloboma 12 | Enrichment | CDON | 2.12 |
| 105 | Pituitary stalk interruption syndrome | Enrichment | CDON | 2.08 |
| 106 | Coloboma of macula | Enrichment | CDON | 2.05 |
| 107 | Capillary malformations, congenital | Enrichment | PIK3CA | 2.05 |
| 108 | Hemimegalencephaly | Enrichment | PIK3CA | 2.05 |
| 109 | Rare isolated myopia | Enrichment | LRPAP1 | 2.05 |
| 110 | Rhabdomyosarcoma | Enrichment | PTCH1 | 2.03 |
| 111 | Atrial septal defect 1 | Enrichment | TGFB2 | 1.98 |
| 112 | Klippel-trenaunay-weber syndrome | Enrichment | PIK3CA | 1.98 |
| 113 | Cowden syndrome 1 | Enrichment | PIK3CA | 1.98 |
| 114 | Hemihyperplasia, isolated | Enrichment | PIK3CA | 1.98 |
| 115 | Lung squamous cell carcinoma | Enrichment | PIK3CA | 1.98 |
| 116 | Nevus, epidermal | Enrichment | PIK3CA | 1.91 |
| 117 | Capillary malformation-arteriovenous malformation 1 | Enrichment | PIK3CA | 1.91 |
| 118 | Gallbladder cancer | Enrichment | PIK3CA | 1.91 |
| 119 | Microphthalmia | Enrichment | PTCH1 | 1.89 |
| 120 | Combined pituitary hormone deficiency | Enrichment | GLI2 | 1.85 |
| 121 | Loeys-dietz syndrome | Enrichment | TGFB2 | 1.80 |
| 122 | Arteriovenous malformation | Enrichment | PIK3CA | 1.80 |
| 123 | Adult hepatocellular carcinoma | Enrichment | PIK3CA | 1.80 |
| 124 | Marfan syndrome | Enrichment | TGFB2 | 1.76 |
| 125 | Myopathy, x-linked, with excessive autophagy | Enrichment | PIK3CA | 1.76 |
| 126 | Autosomal non-syndromic agammaglobulinemia | Enrichment | PIK3R1 | 1.76 |
| 127 | Lung non-small cell carcinoma | Enrichment | PIK3CA | 1.71 |
| 128 | Lip and oral cavity carcinoma | Enrichment | PIK3CA | 1.68 |
| 129 | Diaphragmatic hernia, congenital | Enrichment | GLI3 | 1.64 |
| 130 | Lynch syndrome | Enrichment | PIK3CA | 1.58 |
| 131 | Hereditary breast ovarian cancer syndrome | Enrichment | PTCH1 | 1.50 |
| 132 | Ehlers-danlos syndrome | Enrichment | TGFB2 | 1.48 |
| 133 | Endometrial cancer | Enrichment | PIK3CA | 1.44 |
| 134 | Hepatocellular carcinoma | Enrichment | PIK3CA | 1.42 |
| 135 | Precursor t-cell acute lymphoblastic leukemia | Enrichment | STIL | 1.40 |
| 136 | Autism | Enrichment | SHH | 1.38 |
| 137 | Jeune thoracic dystrophy | Enrichment | GRK2 | 1.36 |
| 138 | Asphyxiating thoracic dystrophy | Enrichment | GRK2 | 1.31 |
| 139 | Bladder cancer | Enrichment | PIK3CA | 1.30 |
| 140 | Prostate cancer | Enrichment | PIK3CA | 1.30 |
| 141 | Lung cancer | Enrichment | PIK3CA | 1.26 |
| 142 | Primary autosomal recessive microcephaly | Enrichment | STIL | 1.26 |
| 143 | Short-rib thoracic dysplasia 1 with or without polydactyly | Enrichment | GRK2 | 1.25 |
| 144 | Gastric cancer | Enrichment | PIK3CA | 1.13 |
| 145 | Familial thoracic aortic aneurysm and aortic dissection | Enrichment | TGFB2 | 1.12 |
| 146 | Inherited cancer-predisposing syndrome | Enrichment | PTCH1 | 1.12 |
| 147 | Hypertelorism | Enrichment | PIK3CA | 1.05 |
| 148 | Male infertility with azoospermia or oligozoospermia due to single gene mutation | Enrichment | GLI2 | 1.02 |
| 149 | Hereditary retinal dystrophy | Enrichment | LRP2 | 0.39 |
| 150 | Fundus dystrophy | Enrichment | LRP2 | 0.39 |