| 1 | Septopreoptic holoprosencephaly | Enrichment | GLI2, PTCH1, SHH | 5.61 |
| 2 | Midline interhemispheric variant of holoprosencephaly | Enrichment | GLI2, PTCH1, SHH | 5.61 |
| 3 | Microform holoprosencephaly | Enrichment | GLI2, PTCH1, SHH | 5.52 |
| 4 | Lobar holoprosencephaly | Enrichment | GLI2, PTCH1, SHH | 5.52 |
| 5 | Split hand-foot malformation | Enrichment | FGFR2, LEF1 | 5.49 |
| 6 | Alobar holoprosencephaly | Enrichment | GLI2, PTCH1, SHH | 5.43 |
| 7 | Semilobar holoprosencephaly | Enrichment | GLI2, PTCH1, SHH | 5.35 |
| 8 | Polydactyly, preaxial ii | Enrichment | PTCH1, SHH | 4.71 |
| 9 | Ectodermal dysplasia 10b, hypohidrotic/hair/tooth type, autosomal recessive | Enrichment | EDA, EDAR | 4.71 |
| 10 | Ectodermal dysplasia | Enrichment | EDA, EDAR | 4.71 |
| 11 | Split-hand/foot malformation 1 | Enrichment | FGFR2, LEF1 | 4.31 |
| 12 | Cleft lip/palate | Enrichment | BMP4, PDGFRA | 3.53 |
| 13 | Polydactyly, postaxial, type a1 | Enrichment | GLI1, PTCH1 | 3.47 |
| 14 | Macs syndrome | Enrichment | PTCH1, SHH | 3.22 |
| 15 | Craniosynostosis | Enrichment | FGFR2, GLI2 | 3.22 |
| 16 | Tooth agenesis | Enrichment | EDA, EDAR | 3.13 |
| 17 | Holoprosencephaly 3 | Enrichment | SHH | 2.73 |
| 18 | Beare-stevenson cutis gyrata syndrome | Enrichment | FGFR2 | 2.73 |
| 19 | Endosteal hyperostosis, autosomal dominant | Enrichment | LRP5 | 2.73 |
| 20 | Bone mineral density quantitative trait locus 1 | Enrichment | LRP5 | 2.73 |
| 21 | Exudative vitreoretinopathy 4 | Enrichment | LRP5 | 2.73 |
| 22 | Curry-jones syndrome | Enrichment | SMO | 2.73 |
| 23 | Hypereosinophilic syndrome, idiopathic | Enrichment | PDGFRA | 2.73 |
| 24 | Schilbach-rott syndrome | Enrichment | PTCH1 | 2.73 |
| 25 | Scaphocephaly, maxillary retrusion, and impaired intellectual development | Enrichment | FGFR2 | 2.73 |
| 26 | Apert syndrome | Enrichment | FGFR2 | 2.73 |
| 27 | Microphthalmia/coloboma 5 | Enrichment | SHH | 2.73 |
| 28 | Polydactyly, preaxial i | Enrichment | GLI1 | 2.73 |
| 29 | Megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 3 | Enrichment | CCND2 | 2.73 |
| 30 | Gist-plus syndrome | Enrichment | PDGFRA | 2.73 |
| 31 | Culler-jones syndrome | Enrichment | GLI2 | 2.73 |
| 32 | Bent bone dysplasia syndrome 1 | Enrichment | FGFR2 | 2.73 |
| 33 | Ectodermal dysplasia 17 with or without limb malformations | Enrichment | LEF1 | 2.73 |
| 34 | Nephrotic syndrome, type 26 | Enrichment | LAMA5 | 2.73 |
| 35 | Polydactyly, postaxial, type a8 | Enrichment | GLI1 | 2.73 |
| 36 | Microphthalmia, syndromic 6 | Enrichment | BMP4 | 2.73 |
| 37 | Myeloid and lymphoid neoplasms associated with pdgfra rearrangement | Enrichment | PDGFRA | 2.73 |
| 38 | Orofacial cleft 11 | Enrichment | BMP4 | 2.73 |
| 39 | Tooth agenesis, selective, x-linked, 1 | Enrichment | EDA | 2.73 |
| 40 | Osteoporosis-pseudoglioma syndrome | Enrichment | LRP5 | 2.73 |
| 41 | Polycystic liver disease 4 with or without kidney cysts | Enrichment | LRP5 | 2.73 |
| 42 | Hair morphology 1 | Enrichment | EDAR | 2.73 |
| 43 | Holoprosencephaly 9 | Enrichment | GLI2 | 2.73 |
| 44 | Bent bone dysplasia syndrome 2 | Enrichment | LAMA5 | 2.73 |
| 45 | Lrp5-related primary osteoporosis | Enrichment | LRP5 | 2.73 |
| 46 | Turner syndrome | Enrichment | PTCH1 | 2.73 |
| 47 | Monosomy 9q22.3 | Enrichment | PTCH1 | 2.73 |
| 48 | Osteosclerosis-developmental delay-craniosynostosis syndrome | Enrichment | LRP5 | 2.73 |
| 49 | Postaxial polydactyly-anterior pituitary anomalies-facial dysmorphism syndrome | Enrichment | GLI2 | 2.73 |
| 50 | Lama5-related multisystemic syndrome | Enrichment | LAMA5 | 2.73 |
| 51 | Non-syndromic unicoronal craniosynostosis | Enrichment | FGFR2 | 2.73 |
| 52 | Autosomal dominant preaxial polydactyly-upperback hypertrichosis syndrome | Enrichment | SHH | 2.73 |
| 53 | Ectrodactyly and ectodermal dysplasia without cleft lip/palate | Enrichment | LEF1 | 2.43 |
| 54 | Burkitt lymphoma | Enrichment | MYC | 2.43 |
| 55 | Van buchem disease | Enrichment | LRP5 | 2.43 |
| 56 | Pallister-hall-like syndrome | Enrichment | SMO | 2.43 |
| 57 | Aural atresia, congenital | Enrichment | FGFR2 | 2.43 |
| 58 | Pfeiffer syndrome | Enrichment | FGFR2 | 2.43 |
| 59 | Jackson-weiss syndrome | Enrichment | FGFR2 | 2.43 |
| 60 | Solitary median maxillary central incisor | Enrichment | SHH | 2.43 |
| 61 | White-sutton syndrome | Enrichment | GLI2 | 2.43 |
| 62 | Immunodeficiency, common variable, 12, with autoimmunity | Enrichment | NFKB1 | 2.43 |
| 63 | Antley-bixler syndrome without genital anomalies or disordered steroidogenesis | Enrichment | FGFR2 | 2.43 |
| 64 | Ectodermal dysplasia 1, hypohidrotic, x-linked | Enrichment | EDA | 2.43 |
| 65 | Postaxial polydactyly type b | Enrichment | GLI1 | 2.43 |
| 66 | Autosomal dominant nonsyndromic deafness | Enrichment | FGFR2 | 2.43 |
| 67 | Chronic eosinophilic leukemia | Enrichment | PDGFRA | 2.43 |
| 68 | B-lymphoblastic leukemia/lymphoma with recurrent genetic abnormality | Enrichment | PDGFRA | 2.43 |
| 69 | Osteosclerosis | Enrichment | LRP5 | 2.43 |
| 70 | Common variable immunodeficiency 12 | Enrichment | NFKB1 | 2.43 |
| 71 | Isolated radial hemimelia | Enrichment | SHH | 2.43 |
| 72 | Crouzon syndrome | Enrichment | FGFR2 | 2.26 |
| 73 | Lacrimoauriculodentodigital syndrome 1 | Enrichment | FGFR2 | 2.26 |
| 74 | Syndactyly, type iv | Enrichment | SHH | 2.26 |
| 75 | Tooth agenesis, selective, 2 | Enrichment | EDA | 2.26 |
| 76 | Osteopetrosis, autosomal dominant 1 | Enrichment | LRP5 | 2.26 |
| 77 | Holoprosencephaly 7 | Enrichment | PTCH1 | 2.26 |
| 78 | Ectodermal dysplasia 11b, hypohidrotic/hair/tooth type, autosomal recessive | Enrichment | EDAR | 2.26 |
| 79 | High-grade b-cell lymphoma double-hit/triple-hit | Enrichment | MYC | 2.26 |
| 80 | Hypoplastic or aplastic tibia with polydactyly | Enrichment | SHH | 2.26 |
| 81 | Robinow syndrome, autosomal dominant 1 | Enrichment | WNT5A | 2.13 |
| 82 | Schizencephaly | Enrichment | SHH | 2.13 |
| 83 | Megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 1 | Enrichment | CCND2 | 2.13 |
| 84 | Saethre-chotzen syndrome | Enrichment | FGFR2 | 2.13 |
| 85 | Mantle cell lymphoma | Enrichment | CCND1 | 2.13 |
| 86 | Retinopathy of prematurity | Enrichment | LRP5 | 2.13 |
| 87 | Autosomal dominant robinow syndrome | Enrichment | WNT5A | 2.13 |
| 88 | Glioma | Enrichment | FGFR2 | 2.13 |
| 89 | Vitreoretinopathy | Enrichment | LRP5 | 2.13 |
| 90 | Ectodermal dysplasia 10a, hypohidrotic/hair/nail type, autosomal dominant | Enrichment | EDAR | 2.04 |
| 91 | Hemifacial hyperplasia | Enrichment | FGFR2 | 2.04 |
| 92 | Exudative vitreoretinopathy 1 | Enrichment | LRP5 | 2.04 |
| 93 | Von hippel-lindau syndrome | Enrichment | CCND1 | 2.04 |
| 94 | Robinow syndrome, autosomal recessive 1 | Enrichment | WNT5A | 2.04 |
| 95 | Autosomal recessive hypohidrotic ectodermal dysplasia syndrome | Enrichment | EDAR | 2.04 |
| 96 | Primary hypereosinophilic syndrome | Enrichment | PDGFRA | 2.04 |
| 97 | Basal cell nevus syndrome 1 | Enrichment | PTCH1 | 1.96 |
| 98 | Anterior segment dysgenesis 5 | Enrichment | BMP4 | 1.96 |
| 99 | Basal cell carcinoma 1 | Enrichment | PTCH1 | 1.96 |
| 100 | Autosomal recessive robinow syndrome | Enrichment | WNT5A | 1.96 |
| 101 | Colorectal cancer | Enrichment | CCND1, FGFR2 | 1.96 |
| 102 | Mitochondrial dna depletion syndrome 4a | Enrichment | EDAR | 1.89 |
| 103 | Gastrointestinal stromal tumor | Enrichment | PDGFRA | 1.89 |
| 104 | Common variable immunodeficiency | Enrichment | NFKB1 | 1.89 |
| 105 | Congenital hydrocephalus | Enrichment | PTCH1 | 1.89 |
| 106 | Overgrowth syndrome | Enrichment | PTCH1 | 1.89 |
| 107 | Mitochondrial dna depletion syndrome 4b | Enrichment | EDAR | 1.83 |
| 108 | Exudative vitreoretinopathy | Enrichment | LRP5 | 1.83 |
| 109 | Combined pituitary hormone deficiency | Enrichment | GLI2 | 1.83 |
| 110 | Ovarian cancer | Enrichment | PDGFRA, PTCH1 | 1.83 |
| 111 | Tooth agenesis, selective, 1 | Enrichment | EDA | 1.78 |
| 112 | Ellis-van creveld syndrome | Enrichment | GLI1 | 1.78 |
| 113 | Leukemia, chronic lymphocytic | Enrichment | CCND1 | 1.74 |
| 114 | Meier-gorlin syndrome 1 | Enrichment | FGFR2 | 1.74 |
| 115 | Peters-plus syndrome | Enrichment | BMP4 | 1.74 |
| 116 | Ciliary dyskinesia, primary, 3 | Enrichment | NFKB1 | 1.74 |
| 117 | Stickler syndrome | Enrichment | BMP4 | 1.74 |
| 118 | Presynaptic congenital myasthenic syndromes | Enrichment | LAMA5 | 1.70 |
| 119 | Septooptic dysplasia | Enrichment | SHH | 1.66 |
| 120 | Renal hypodysplasia/aplasia 3 | Enrichment | BMP4 | 1.66 |
| 121 | Meningioma | Enrichment | SMO | 1.66 |
| 122 | Neural tube defects | Enrichment | ITGB1 | 1.63 |
| 123 | Inherited cancer-predisposing syndrome | Enrichment | PDGFRA, PTCH1 | 1.61 |
| 124 | Multiple sclerosis | Enrichment | LAMA5 | 1.59 |
| 125 | Osteoporosis | Enrichment | LRP5 | 1.59 |
| 126 | Medulloblastoma | Enrichment | PTCH1 | 1.59 |
| 127 | Hydrocephalus | Enrichment | FGFR2 | 1.56 |
| 128 | Rhabdomyosarcoma | Enrichment | PTCH1 | 1.54 |
| 129 | Polycystic liver disease | Enrichment | LRP5 | 1.51 |
| 130 | Autosomal dominant polycystic liver disease | Enrichment | LRP5 | 1.51 |
| 131 | Endometrial cancer | Enrichment | FGFR2 | 1.42 |
| 132 | Microphthalmia | Enrichment | PTCH1 | 1.40 |
| 133 | Brittle bone disorder | Enrichment | LRP5 | 1.38 |
| 134 | Precursor t-cell acute lymphoblastic leukemia | Enrichment | MYC | 1.38 |
| 135 | Hirschsprung disease 1 | Enrichment | SMO | 1.28 |
| 136 | Genetic steroid-resistant nephrotic syndrome | Enrichment | LAMA5 | 1.22 |
| 137 | Gastric cancer | Enrichment | FGFR2 | 1.12 |
| 138 | Nephrotic syndrome | Enrichment | LAMA5 | 1.12 |
| 139 | Hypertelorism | Enrichment | FGFR2 | 1.04 |
| 140 | Hereditary breast ovarian cancer syndrome | Enrichment | PTCH1 | 1.01 |
| 141 | Myeloma, multiple | Enrichment | CCND1 | 1.01 |
| 142 | Male infertility with azoospermia or oligozoospermia due to single gene mutation | Enrichment | GLI2 | 1.01 |
| 143 | Autism | Enrichment | SHH | 0.90 |
| 144 | Hereditary retinal dystrophy | Enrichment | LRP5 | 0.38 |
| 145 | Fundus dystrophy | Enrichment | LRP5 | 0.38 |