| Gene symbol | Gene name | Chr. | Entrez ID | UniProt ID | Cleft type | Species | Evidence | Details |
|---|---|---|---|---|---|---|---|---|
| RARA | Retinoic acid receptor alpha | 17 | 5914 | P10276 | CPO,CL/P | Homo sapiens | More>> | |
| RUNX2 | Runt-related transcription factor 2 | 6 | 860 | Q13950 | CL/P | Homo sapiens | More>> | |
| RYK | Tyrosine-protein kinase RYK | 3 | 6259 | P34925 | CPO,CL/P | Homo sapiens | More>> | |
| TBX22 | T-box transcription factor TBX22 | X | 50945 | Q9Y458 | CPO,CL/P | Homo sapiens | More>> | |
| TGFA | Protransforming growth factor alpha | 2 | 7039 | P01135 | CPO,CL/P | Homo sapiens | More>> | |
| TGFB3 | Transforming growth factor beta-3 proprotein | 14 | 7043 | P10600 | CPO,CL/P | Homo sapiens | More>> | |
| TYMS | Thymidylate synthase | 18 | 7298 | P04818 | CPO,CL/P | Homo sapiens | More>> | |
| VAX1 | Ventral anterior homeobox 1 | 10 | 11023 | Q5SQQ9 | CL/P | Homo sapiens | More>> | |
| WNT10A | Protein Wnt-10a | 2 | 80326 | Q9GZT5 | CPO,CL/P | Homo sapiens | More>> | |
| WNT3 | Proto-oncogene Wnt-3 | 17 | 7473 | P56703 | CL/P | Homo sapiens | More>> | |
| ZNF385B | Zinc finger protein 385B | 2 | 151126 | Q569K4 | CPO,CL/P | Homo sapiens | More>> | |
| ARHGAP29 | Rho GTPase-activating protein 29 | 1 | 9411 | Q52LW3 | CPO,CL/P | Homo sapiens | More>> | |
| ASS1 | Argininosuccinate synthase | 9 | 445 | P00966 | CL/P | Homo sapiens | More>> | |
| BCL3 | B-cell lymphoma 3 protein | 19 | 602 | P20749 | CL/P | Homo sapiens | More>> | |
| BLM | Bloom syndrome protein | 15 | 641 | P54132 | CL/P | Homo sapiens | More>> | |
| BMP4 | Bone morphogenetic protein 4 | 14 | 652 | P12644 | CPO,CL/P | Homo sapiens | More>> | |
| COL4A3 | Collagen alpha-3(IV) chain | 2 | 1285 | Q01955 | CPO,CL/P | Homo sapiens | More>> | |
| CRISPLD2 | Cysteine-rich secretory protein LCCL domain-containing 2 | 16 | 83716 | Q9H0B8 | CPO,CL/P | Homo sapiens | More>> | |
| CYP1A1 | Cytochrome P450 1A1 | 15 | 1543 | P04798 | CPO,CL/P | Homo sapiens | More>> | |
| CYP2E1 | Cytochrome P450 2E1 | 10 | 1571 | P05181 | CPO,CL/P | Homo sapiens | More>> | |
| DVL2 | Segment polarity protein dishevelled homolog DVL-2 | 17 | 1856 | O14641 | CL/P | Homo sapiens | More>> | |
| EFNB1 | Ephrin-B1 | X | 1947 | P98172 | CPO,CL/P | Homo sapiens | More>> | |
| EVC | Ellis-van Creveld syndrome protein | 4 | 2121 | P57679 | CPO,CL/P | Homo sapiens | More>> | |
| EYA1 | Eyes absent homolog 1 | 8 | 2138 | Q99502 | CPO,CL/P | Homo sapiens | More>> | |
| F13A1 | Coagulation factor XIII A chain | 6 | 2162 | P00488 | CPO,CL/P | Homo sapiens | More>> | |
| FGF1 | Fibroblast growth factor 1 | 5 | 2246 | P05230 | CPO,CL/P | Homo sapiens | More>> | |
| FGFR1 | Fibroblast growth factor receptor 1 | 8 | 2260 | P11362 | CL/P | Homo sapiens | More>> | |
| FOXE1 | Forkhead box protein E1 | 9 | 2304 | O00358 | CPO,CL/P | Homo sapiens | More>> | |
| FZD6 | Frizzled-6 | 8 | 8323 | O60353 | CL/P | Homo sapiens | More>> | |
| GAD1 | Glutamate decarboxylase 1 | 2 | 2571 | Q99259 | CL/P | Homo sapiens | More>> | |
| GREM1 | Gremlin-1 | 15 | 26585 | O60565 | CL/P | Homo sapiens | More>> | |
| IRF6 | Interferon regulatory factor 6 | 1 | 3664 | O14896 | CPO,CL/P | Homo sapiens | More>> | |
| JARID2 | Protein Jumonji | 6 | 3720 | Q92833 | CPO,CL/P | Homo sapiens | More>> | |
| MAFB | Transcription factor MafB | 20 | 9935 | Q9Y5Q3 | CPO,CL/P | Homo sapiens | More>> | |
| MMP3 | Stromelysin-1 | 11 | 4314 | P08254 | CPO,CL/P | Homo sapiens | More>> | |
| MSX1 | Homeobox protein MSX-1 | 4 | 4487 | P28360 | CPO,CL/P | Homo sapiens | More>> | |
| MTHFR | Methylenetetrahydrofolate reductase | 1 | 4524 | P42898 | CPO,CL/P | Homo sapiens | More>> | |
| MTRR | Methionine synthase reductase | 5 | 4552 | Q9UBK8 | CPO,CL/P | Homo sapiens | More>> | |
| MYH9 | Myosin-9 | 22 | 4627 | P35579 | CPO,CL/P | Homo sapiens | More>> | |
| PAH | Phenylalanine-4-hydroxylase | 12 | 5053 | P00439 | CL/P | Homo sapiens | More>> | |
| PAX7 | Paired box protein Pax-7 | 1 | 5081 | P23759 | CPO,CL/P | Homo sapiens | More>> | |
| PAX9 | Paired box protein Pax-9 | 14 | 5083 | P55771 | CPO,CL/P | Homo sapiens | More>> | |
| PHF8 | Histone lysine demethylase PHF8 | X | 23133 | Q9UPP1 | CPO,CL/P | Homo sapiens | More>> | |
| ADH1C | Alcohol dehydrogenase 1C | 4 | 126 | P00326 | CPO,CL/P | Homo sapiens | More>> | |
| CBS | Cystathionine beta-synthase | 21 | 875 | P35520 | CPO,CL/P | Homo sapiens | More>> | |
| CDH1 | Cadherin-1 | 16 | 999 | P12830 | CPO,CL/P | Homo sapiens | More>> | |
| DHFR | Dihydrofolate reductase | 5 | 1719 | P00374 | CPO,CL/P | Homo sapiens | More>> | |
| DMD | Dystrophin | X | 1756 | P11532 | CL/P | Homo sapiens | More>> | |
| GABRB3 | Gamma-aminobutyric acid receptor subunit beta-3 | 15 | 2562 | P28472 | CL/P | Homo sapiens | More>> | |
| GSTP1 | Glutathione S-transferase P | 11 | 2950 | P09211 | CPO,CL/P | Homo sapiens | More>> | |
| GSTT1 | Glutathione S-transferase theta-1 | 22 | 2952 | P30711 | CL/P | Homo sapiens | More>> | |
| JAG2 | Protein jagged-2 | 14 | 3714 | Q9Y219 | CPO,CL/P | Homo sapiens | More>> | |
| MTHFD1 | C-1-tetrahydrofolate synthase, cytoplasmic | 14 | 4522 | P11586 | CPO,CL/P | Homo sapiens | More>> | |
| NAT1 | Arylamine N-acetyltransferase 1 | 8 | 9 | P18440 | CPO,CL/P | Homo sapiens | More>> | |
| TPM1 | Tropomyosin alpha-1 chain | 15 | 7168 | P09493 | CPO,CL/P | Homo sapiens | More>> | |
| Ermp1 | Endoplasmic reticulum metallopeptidase 1 | 19 | 226090 | Q3UVK0 | CPO,CLP,CLO | Mus musculus | More>> | |
| Esrp2 | Epithelial splicing regulatory protein 2 | 8 | 77411 | Q8K0G8 | CLP | Mus musculus | More>> | |
| Fgf8 | Fibroblast growth factor 8 | 19 | 14179 | P37237 | CPO,CLP | Mus musculus | More>> | |
| Folr1 | Folate receptor alpha | 7 | 14275 | P35846 | CPO,CLP,CLO | Mus musculus | More>> | |
| Gli3 | Transcriptional activator GLI3 | 13 | 14634 | Q61602 | CPO,CLO | Mus musculus | More>> | |
| Hhat | Protein-cysteine N-palmitoyltransferase HHAT | 1 | 226861 | Q8BMT9 | CLP | Mus musculus | More>> | |
| Ift88 | Intraflagellar transport protein 88 homolog | 21821 | Q61371 | CPO,CLP,CLO | Mus musculus | More>> | ||
| Ihh | Indian hedgehog protein | 1 | 16147 | P97812 | CLP | Mus musculus | More>> | |
| Kynu | Kynureninase | 70789 | Q9CXF0 | CLP,CLO | Mus musculus | More>> | ||
| Mks1 | Meckel syndrome type 1 protein homolog | 11 | 380718 | Q5SW45 | CPO,CLP,CLO | Mus musculus | More>> | |
| Nodal | Nodal | 10 | 18119 | P43021 | CLO | Mus musculus | More>> | |
| Pbx1 | Pre-B-cell leukemia transcription factor 1 | 1 | 18514 | P41778 | CPO,CLP,CLO | Mus musculus | More>> | |
| Pbx3 | Pre-B-cell leukemia transcription factor 3 | 2 | 18516 | O35317 | CPO,CLP | Mus musculus | More>> | |
| Pgap2 | Post-GPI attachment to proteins factor 2 | 7 | 233575 | Q3TQR0 | CPO,CLP,CLO | Mus musculus | More>> | |
| Rpgrip1l | Protein fantom | 8 | 244585 | Q8CG73 | CPO,CLP,CLO | Mus musculus | More>> | |
| Rpl38 | 60S ribosomal protein L38 | 11 | 67671 | Q9JJI8 | CPO,CLP,CLO | Mus musculus | More>> | |
| Rspo2 | R-spondin-2 | 15 | 239405 | Q8BFU0 | CPO,CLP | Mus musculus | More>> | |
| Sox11 | Transcription factor SOX-11 | 12 | 20666 | Q7M6Y2 | CPO,CLP | Mus musculus | More>> | |
| Sp8 | Transcription factor Sp8 | 12 | 320145 | Q8BMJ8 | CPO,CLO | Mus musculus | More>> | |
| Tbx10 | T-box transcription factor TBX10 | 19 | 109575 | Q810F8 | CLP | Mus musculus | More>> | |
| Tp53 | Cellular tumor antigen p53 | 11 | 22059 | P02340 | CPO,CLP | Mus musculus | More>> | |
| Wdr19 | WD repeat-containing protein 19 | 5 | 213081 | Q3UGF1 | CPO,CLP | Mus musculus | More>> | |
| Zeb1 | Zinc finger E-box-binding homeobox 1 | 18 | 21417 | Q64318 | CPO,CLP | Mus musculus | More>> | |
| Bmp4 | Bone morphogenetic protein 4 | 14 | 12159 | P21275 | CPO,CLO | Mus musculus | More>> | |
| Msx1 | Homeobox protein MSX-1 | 5 | 17701 | P13297 | CPO,CLP | Mus musculus | More>> | |
| Pax9 | Paired box protein Pax-9 | 12 | 18511 | P47242 | CPO,CLP | Mus musculus | More>> | |
| Tp63 | Tumor protein 63 | 16 | 22061 | O88898 | CPO,CLP | Mus musculus | More>> | |
| Wnt9b | Protein Wnt-9b | 11 | 22412 | O35468 | CLP,CLO | Mus musculus | More>> | |
| Aldh1a2 | Retinal dehydrogenase 2 | 9 | 19378 | Q62148 | CPO,CLO | Mus musculus | More>> | |
| Aldh1a3 | Aldehyde dehydrogenase family 1 member A3 | 7 | 56847 | Q9JHW9 | CPO,CLO | Mus musculus | More>> | |
| Bbs7 | Bardet-Biedl syndrome 7 protein homolog | 3 | 71492 | Q8K2G4 | CPO,CLP,CLO | Mus musculus | More>> | |
| Bmpr1a | Bone morphogenetic protein receptor type-1A | 14 | 12166 | P36895 | CPO,CLP | Mus musculus | More>> | |
| Cdc42 | Cell division control protein 42 homolog | 4 | 12540 | P60766 | CPO,CLP | Mus musculus | More>> | |
| Cplane1 | Ciliogenesis and planar polarity effector 1 | 15 | 73692 | Q8CE72 | CLP | Mus musculus | More>> | |
| Cplane2 | Ciliogenesis and planar polarity effector 2 | 4 | 76166 | A2A825 | CLO | Mus musculus | More>> | |
| Ctnnb1 | Catenin beta-1 | 9 | 12387 | Q02248 | CPO,CLP | Mus musculus | More>> | |
| Dzip1l | Zinc finger protein DZIP1L | 9 | 72507 | Q499E4 | CPO,CLP | Mus musculus | More>> | |
| Ednrb | Endothelin receptor type B | 14 | 13618 | P48302 | CPO,CLP | Mus musculus | More>> | |
| Esrp1 | Epithelial splicing regulatory protein 1 | 4 | 207920 | Q3US41 | CLP | Mus musculus | More>> | |
| Gdf1 | Embryonic growth/differentiation factor 1 | 8 | 14559 | P20863 | CLO | Mus musculus | More>> | |
| Kif3a | Kinesin-like protein KIF3A | 11 | 16568 | P28741 | CPO,CLP | Mus musculus | More>> | |
| Lrp6 | Low-density lipoprotein receptor-related protein 6 | 16974 | O88572 | CPO,CLP | Mus musculus | More>> | ||
| Pbx2 | Pre-B-cell leukemia transcription factor 2 | 17 | 18515 | O35984 | CPO,CLP | Mus musculus | More>> | |
| Ptch1 | Protein patched homolog 1 | 13 | 19206 | Q61115 | CPO,CLP,CLO | Mus musculus | More>> | |
| Tbx1 | T-box transcription factor TBX1 | 21380 | P70323 | CPO,CLP,CLO | Mus musculus | More>> | ||
| Tfap2a | Transcription factor AP-2-alpha | 21418 | P34056 | CPO,CLP | Mus musculus | More>> | ||
| Tgfbr1 | TGF-beta receptor type-1 | 4 | 21812 | Q64729 | CPO,CLP,CLO | Mus musculus | More>> |
Abbreviation :
Chr. Chromosome. CLO : cleft lip only. CPO : cleft palate only.
CLP : cleft lip and palate. CL/P : cleft lip with/without cleft palate.