| Gene | HGNC ID | Core function in odontogenesis | Reported inheritance in TA | Syndromic / non-syndromic association | Teeth/patterns most often affected | OMIM-associated condition(s) noted in gathered evidence | Key 2020–2025 references |
|---|---:|---|---|---|---|---|---|
| EDA | HGNC:3157 | Encodes ectodysplasin A, a TNF-family ligand that binds EDAR and activates NF-κB signaling required for ectodermal appendage and tooth development | X-linked; can show variable expressivity | Both; selective tooth agenesis and X-linked hypohidrotic ectodermal dysplasia | Strong anterior pattern; mandibular deciduous central incisors, mandibular lateral incisors, maxillary lateral incisors; average 15.4 missing deciduous teeth in one 2024 cohort | XLHED OMIM #305100; selective tooth agenesis locus on Xq13.1 | Su 2024; Modafferi 2025 (pqac-00000011, pqac-00000009) |
| MSX1 | HGNC:7391 | Homeobox transcription factor; regulator within BMP/Wnt-linked craniofacial and tooth development programs | Usually autosomal dominant | Both; isolated TA plus syndromic/cleft-associated forms | Often isolated tooth deficiencies; classic association with familial oligodontia; pattern not fully specified in gathered passages | Selective tooth agenesis 1 / hypodontia OMIM #106600; orofacial cleft OMIM #608874; Witkop syndrome OMIM #189500; Wolf-Hirschhorn syndrome OMIM #194190 | Meade 2023; Modafferi 2025 (pqac-00000004, pqac-00000009) |
| WNT10A | HGNC:12722 | WNT ligand central to Wnt/β-catenin signaling during epithelial-mesenchymal interactions in tooth morphogenesis | Autosomal dominant and autosomal recessive reported | Both; common cause of isolated hypodontia/oligodontia and ectodermal dysplasia-related disease | Frequently implicated in permanent tooth agenesis; specific tooth pattern not detailed in gathered passages | Odonto-onycho-dermal dysplasia / ectodermal dysplasia 16; Schöpf-Schulz-Passarge syndrome | Modafferi 2025; Raju 2024; Song 2023 (pqac-00000009, pqac-00000008) |
| PAX9 | HGNC:8616 | Paired-box transcription factor active in dental mesenchyme; disturbances can arrest development at bud stage | Autosomal dominant | Primarily non-syndromic in gathered evidence | Strong association with missing molars; also represented among severe deciduous TA cases | Selective tooth agenesis 3 | Meade 2023; Su 2024; Modafferi 2025 (pqac-00000004, pqac-00000011, pqac-00000009) |
| AXIN2 | HGNC:904 | Negative regulator/scaffold in Wnt signaling pathway | Often autosomal dominant in familial TA literature; inheritance not explicitly detailed in gathered excerpts | Primarily non-syndromic but clinically important systemic association | Lower incisor agenesis and some oligodontia forms | Tooth agenesis with colorectal cancer susceptibility association noted; specific OMIM not provided in gathered passages | Meade 2023; Fallea 2025 (pqac-00000004, pqac-00000002) |
| LRP6 | HGNC:6698 | Wnt co-receptor required for effective Wnt pathway activation in tooth development | Autosomal dominant | Both; selective TA and systemic coronary artery disease association | Included among major TA genes; specific tooth pattern not detailed in gathered passages | Selective tooth agenesis; coronary artery disease, autosomal dominant | Modafferi 2025; Fallea 2025 (pqac-00000009, pqac-00000002) |
| PITX2 | HGNC:9004 | Paired-like homeodomain transcription factor involved in craniofacial patterning and tooth morphogenesis | Autosomal dominant | Both; tooth-size/tooth-number anomalies and Axenfeld-Rieger spectrum | Variation in tooth dimensions; can appear in deciduous TA | Axenfeld-Rieger syndrome type 1; ring dermoid of cornea | Modafferi 2025; Su 2024 (pqac-00000009, pqac-00000011) |
| TSPEAR | HGNC:26961 | Protein implicated in ectodermal development; recurrently linked to oligodontia/ectodermal dysplasia phenotypes | Often biallelic / autosomal recessive in reported ectodermal dysplasia cases | Both, but strong syndromic overlap with ectodermal dysplasia | Non-syndromic oligodontia reported; exact tooth pattern not specified in gathered passages | Tooth agenesis selective 10; ectodermal dysplasia-related phenotypes | Modafferi 2025; Bowles 2021 (pqac-00000009) |
| GREM2 | HGNC:16008 | BMP antagonist (DAN family) modulating developmental signaling balance in odontogenesis | Autosomal dominant | Non-syndromic selective TA in gathered evidence | Specific tooth pattern not detailed in gathered passages | Selective tooth agenesis 9 | Modafferi 2025; Fallea 2025 (pqac-00000009, pqac-00000008) |
| BMP4 | HGNC:1071 | BMP ligand in developmental signaling networks controlling tooth morphogenesis | Not specified in gathered passages | Both candidate/causal roles reported | Rarely represented in severe deciduous TA cohort; specific tooth pattern not detailed | Not specified in gathered passages | Su 2024; BMP pathway reviews 2023 (pqac-00000011, pqac-00000008) |
| EDAR | HGNC:2895 | Receptor for EDA; activates downstream NF-κB signaling essential for ectodermal appendage development | Can contribute in ectodermal/EDA-pathway TA; inheritance not specified in gathered excerpts | Both, especially syndromic ectodermal dysplasia spectrum | Specific tooth pattern not detailed in gathered passages | Ectodysplasin/EDAR pathway-associated TA and ectodermal dysplasia | Fallea 2025; Su 2024 (pqac-00000002, pqac-00000011) |
| EDARADD | HGNC:2897 | EDAR-associated death domain adaptor; transduces EDA–EDAR signaling to NF-κB | Inheritance not specified in gathered passages | Both, mainly ectodermal dysplasia/TA pathway gene | Rare cause in deciduous TA cohort; specific tooth pattern not detailed | EDA-pathway ectodermal dysplasia / tooth agenesis association | Fallea 2025; Su 2024 (pqac-00000002, pqac-00000011) |
| KREMEN1 | HGNC:21241 | Kringle-domain transmembrane protein that modulates Wnt signaling | Autosomal recessive | Both; hair/tooth ectodermal dysplasia phenotype emphasized | Specific tooth pattern not detailed in gathered passages | Ectodermal dysplasia 13, hair/tooth type | Modafferi 2025 (pqac-00000009) |
| SMOC2 | HGNC:11186 | SPARC-related modular calcium-binding extracellular protein involved in craniofacial/dental matrix biology | Autosomal recessive | Syndromic/complex dental phenotype and non-isolated severe dental anomaly | Associated with microdontia and misshapen teeth in addition to reduced tooth number | Dentin dysplasia type I with microdontia and misshapen teeth | Modafferi 2025; Fallea 2025 (pqac-00000009, pqac-00000008) |


*Table: This table summarizes the principal genes implicated in tooth agenesis, integrating gene function, inheritance, clinical context, and characteristic dental patterns from the gathered 2020–2025 literature. It is useful for building disease knowledge-base entries and for prioritizing diagnostic genes in syndromic and non-syndromic cases.*