| Gene |
Chromosome |
Location |
Syndrome |
| (der 11) | 22 | extra | Emanuel syndrome | |
| (der 22) | 11 | extra | Emanuel syndrome | |
| ALX1 | 12 | q21.31 | Frontonasal dysplasia | |
| ALX3 | 1 | p13.3 | Frontonasal dysplasia | |
| ANOS1 | 23 | p22.32 | Kallmann syndrome types 1 and 2 | |
| B3GLCT | 13 | q12.3 | Peters plus syndrome | |
| CEP120 | 5 | q23.2 | Short-rib thoracic dysplasia 13 | |
| CHD7 | 8 | q12.2 | CHARGE syndrome | |
| COLEC11 | 2 | p25.3 | Carnevale syndrome | |
| CPCMR | 15 | q14 | Cleft palate cardiac defects and mental retardation | |
| DHODH | 16 | q22 | Miller syndrome | |
| EMG1 | 12 | p13.3 | Bowen-Conradi syndrome | |
| ESCO2 | 8 | p21.1 | Roberts syndrome | |
| FGD1 | 23 | p11.21 | Aarskog-Scott syndrome | |
| FGF10 | 5 | p12-13 | Crouzon syndrome | |
| FGFR1 | 8 | p11.22-23 | Kallmann syndrome types 1 and 2 | |
| FGFR2 | 10 | q26 | Crouzon syndrome | |
| FGFR3 | 4 | p16.3 | Crouzon syndrome | |
| FRAS1 | 4 | q21.21 | Fraser syndrome | |
| FREM2 | 13 | q13.3 | Fraser syndrome | |
| PVRL1 | 11 | q23.3 | Non-syndromic orofacial cleft 7 | |
| RPL11 | 1 | p35-36.1 | Diamond-Blackfan anemia | |
| RPL35A | 3 | q29 | Diamond-Blackfan anemia | |
| RPL5 | 1 | p22.1 | Diamond-Blackfan anemia | |
| RPS10 | 6 | p21.31 | Diamond-Blackfan anemia | |
| RPS17 | 15 | q21.3 | Diamond-Blackfan anemia | |
| RPS19 | 19 | q13.2 | Diamond-Blackfan anemia | |
| RPS24 | 10 | q22 | Diamond-Blackfan anemia | |
| RPS26 | 12 | q13 | Diamond-Blackfan anemia | |
| RPS7 | 2 | p25 | Diamond-Blackfan anemia | |
| SCARF2 | 22 | q11.21 | Van den Ende-Gupta syndrome | |
| SEMA3E | 7 | q21.11 | CHARGE syndrome | |
| SHH | 7 | q37 | Nonsyndromic holoprosencephaly | |
| SIX3 | 2 | p21 | Nonsyndromic holoprosencephaly | |
| SMAD4 | 18 | q21.1 | Myhre syndrome | |
| SMOC1 | 14 | q24.2 | Ophthalmo-acromelic syndrome | |
| SMS | 23 | p22.1 | Snyder-Robinson syndrome | |
| SPECC1L | 22 | q11.23 | Opitz G/BBB syndrome | |
| SUMO1 | 2 | q33 | Non-syndromic orofacial cleft 10 | |
| TFAP2A | 6 | p24 | Branchio-oculo-facial syndrome | |
| TGIF1 | 18 | p11.3 | Nonsyndromic holoprosencephaly | |
| TP63 | 3 | q28 | Ankyloblepharon-ectodermal defects-cleft lip/palate syndrome | |
| trisomy | 13 | all | Patau syndrome | |
| TXNL4A | 18 | q23 | Burn-McKeown syndrome | |
| unknown | 9 | unknown | Nager syndrome | |
| VAX1 | 10 | q26.1 | Syndromic Microphthalmia | |
| WDR34 | 9 | q34.11 | Short-rib thoracic dysplasia 13 | |
| WDR60 | 7 | q36.3 | Short-rib thoracic dysplasia 13 | |
| WHSC1 | 4 | p16.3 | Wolf-Hirschhorn syndrome | |
| YAP1 | 11 | q13 | Yes associated protein 1 malformation | |
| ZIC2 | 13 | q32 | Nonsyndromic holoprosencephaly | |