| Gene symbol | Full name | OMIM ID (if known) | Associated syndrome / phenotype | Gene function relevant to CL/P | Typical variant type(s) reported | OpenTargets association score | Key evidence |
|---|---|---:|---|---|---|---:|---|
| IRF6 | Interferon regulatory factor 6 | 607199 | Van der Woude syndrome; popliteal pterygium syndrome; syndromic and non-syndromic cleft lip/palate; regulatory variant associated with cleft palate in Finland | Periderm differentiation; epithelial integrity; palatal fusion transcriptional regulator | Heterozygous pathogenic variants; common risk SNPs; regulatory/enhancer variants | 0.57 (cleft lip); 0.42 (cleft lip/palate) | (pqac-00000000, pqac-00000010, pqac-00000012, pqac-00000013, pqac-00000048) |
| MSX1 | Msh homeobox 1 | 142983 | Non-syndromic CL/P; tooth agenesis; rare syndromic and non-syndromic cleft palate/lip-palate | Homeobox transcription factor in craniofacial patterning; regulates epithelial-mesenchymal signaling during palate development | Rare pathogenic coding variants; common susceptibility variants; null alleles in models | 0.47 (cleft lip); 0.77 (cleft lip/palate) | (pqac-00000000, pqac-00000010, pqac-00000012, pqac-00000015, pqac-00000046) |
| BMP4 | Bone morphogenetic protein 4 | 112262 | Cleft lip/palate susceptibility; craniofacial malformations | BMP pathway ligand controlling proliferation, differentiation, apoptosis, and palatal mesenchyme growth | Susceptibility SNPs; missense/duplication evidence in broader craniofacial anomaly literature | 0.74 (cleft lip/palate) | (pqac-00000000, pqac-00000020, pqac-00000025, pqac-00000029) |
| TP63 | Tumor protein p63 | 603273 | EEC syndrome; Hay-Wells syndrome; Rapp-Hodgkin syndrome; CL/P susceptibility | Epithelial development, adhesion, and palatal seam biology; upstream regulator of epithelial differentiation | Rare pathogenic missense / truncating variants; GWAS SNP rs76479869 association | 0.42 (cleft lip); 0.49 (cleft lip/palate) | (pqac-00000000, pqac-00000009, pqac-00000011, pqac-00000030) |
| ARHGAP29 | Rho GTPase activating protein 29 | 610496 | Non-syndromic cleft lip / palate susceptibility | Cytoskeletal / Rho signaling regulator implicated in craniofacial morphogenesis | Rare pathogenic variants; susceptibility variants from sequencing/GWAS-supported studies | 0.61 (cleft lip) | (pqac-00000000, pqac-00000009) |
| CTNND1 | Catenin delta 1 | 601045 | Non-syndromic CL/P; epithelial adhesion-related cleft phenotypes | Cadherin–catenin complex component regulating epithelial adhesion and integrity | Pathogenic/likely pathogenic variants; splice-related dysregulation via ESRP1/2 | 0.51 (cleft lip) | (pqac-00000000, pqac-00000011, pqac-00000026) |
| PAX7 | Paired box 7 | 167410 | Non-syndromic cleft lip susceptibility; frontonasal patterning-related phenotypes | Transcription factor involved in craniofacial/frontonasal mesenchyme development | Common susceptibility variants/SNPs | 0.49 (cleft lip) | (pqac-00000000, pqac-00000009, pqac-00000052) |
| CDH1 | Cadherin 1 | 192090 | Blepharocheilodontic syndrome; cleft lip susceptibility | Cell-cell adhesion protein essential for epithelial integrity | Heterozygous pathogenic variants; likely loss-of-function / missense variants | 0.39 (cleft lip) | (pqac-00000000, pqac-00000010, pqac-00000014) |
| NECTIN1 | Nectin cell adhesion molecule 1 | 600644 | Cleft lip/palate-ectodermal dysplasia syndrome; cleft lip susceptibility | Cell adhesion molecule contributing to epithelial fusion processes | Pathogenic variants in syndromic clefting; curated gene-disease evidence | 0.48 (cleft lip); 0.85 (cleft lip/palate-ectodermal dysplasia syndrome) | (pqac-00000000) |
| NTN1 | Netrin 1 | 601614 | Non-syndromic cleft lip susceptibility | Guidance cue involved in tissue morphogenesis and craniofacial developmental signaling | Common susceptibility variants; sequencing-supported variants | 0.47 (cleft lip) | (pqac-00000000, pqac-00000014) |
| GRHL3 | Grainyhead like transcription factor 3 | 608317 | Cleft palate; downstream effector of IRF6; syndromic/non-syndromic palatal defects | Periderm differentiation and epithelial barrier/fusion regulation | Rare pathogenic variants; GWAS locus evidence for cleft palate | Not listed in retrieved OpenTargets results | (pqac-00000012, pqac-00000041) |
| FOXE1 | Forkhead box E1 | 602617 | Associated with all major OFC types; non-syndromic CL/P susceptibility | Craniofacial developmental transcription factor | Susceptibility SNPs, including rs12347191 near FOXE1 | Not listed in retrieved OpenTargets results | (pqac-00000009, pqac-00000013, pqac-00000016) |
| TGFB3 | Transforming growth factor beta 3 | 190230 | Cleft palate / CL/P susceptibility; smoking-interaction risk locus | Key regulator of palatal shelf adhesion/fusion and MES breakdown | Susceptibility variants/polymorphisms; gene-environment interaction variants | Not listed in retrieved OpenTargets results | (pqac-00000016, pqac-00000020, pqac-00000026) |
| FGFR1 | Fibroblast growth factor receptor 1 | 136350 | CL/P susceptibility; craniofacial developmental anomalies | FGF receptor mediating epithelial-mesenchymal signaling in palatogenesis | Susceptibility variants; rare pathogenic variants in craniofacial syndromes | Not listed in retrieved OpenTargets results | (pqac-00000013, pqac-00000016, pqac-00000031) |
| SUMO1 | Small ubiquitin-like modifier 1 | 601912 | Cleft lip/palate | Post-translational modifier implicated in craniofacial development | Rare pathogenic / copy-number-related evidence in curated datasets | 0.42 (cleft lip/palate) | (pqac-00000000) |


*Table: This table summarizes high-priority genes implicated in cleft lip and/or palate, integrating curated disease-target associations with mechanistic and genetic evidence. It is useful for building a disease knowledge base entry and prioritizing genes for annotation, diagnostics, and pathway analysis.*