Anophthalmia/microphthalmia-esophageal atresia syndrome: genes and variants
Anophthalmia/microphthalmia-esophageal atresia syndrome is linked to 1 analyzed protein (SOX2). 13 DNA variants are known to cause it; 31 more are uncertain, and 0 of those already look disease-causing on computable evidence.
Last updated 2026-09-30. Research information, not medical advice.
Genes linked to Anophthalmia/microphthalmia-esophageal atresia syndrome
SOX2: Transcription factor SOX-2
It maintains neural and embryonic progenitor identity and directs development of the eye, forebrain, pituitary, and other organs. Haploinsufficiency causes SOX2 disorder, frequently with anophthalmia or microphthalmia and variable neurodevelopmental, endocrine, and genital abnormalities.
13 disease-causing and 31 uncertain variants in SOX2 are linked to Anophthalmia/microphthalmia-esophageal atresia syndrome.
Where Anophthalmia/microphthalmia-esophageal atresia syndrome variants cluster
- SOX2 HMG box (positions 41–109): 9 of 13 disease-causing changes, 3.2× more than its size predicts.
Known disease-causing variants in Anophthalmia/microphthalmia-esophageal atresia syndrome
| Variant | Position | Protein part | Clinical label |
|---|---|---|---|
| SOX2 P112L | 112 | Disease-causing (★★) | |
| SOX2 F48S | 48 | HMG box | Disease-causing (★) |
| SOX2 F48V | 48 | HMG box | Disease-causing (★) |
| SOX2 R96P | 96 | HMG box | Disease-causing (★) |
| SOX2 Y110S | 110 | Disease-causing (★) | |
| SOX2 R113W | 113 | Disease-causing (★) | |
| SOX2 A287P | 287 | Disease-causing (★) | |
| SOX2 N46K | 46 | HMG box | Disease-causing |
| SOX2 L97P | 97 | HMG box | Disease-causing |
| SOX2 R98P | 98 | HMG box | Disease-causing |
| SOX2 P44R | 44 | HMG box | Disease-causing |
| SOX2 R56G | 56 | HMG box | Disease-causing |
| SOX2 R74P | 74 | HMG box | Disease-causing |
Which prediction tools work for Anophthalmia/microphthalmia-esophageal atresia syndrome
How often each tool ranks a disease-causing variant above a harmless one (AUROC × 100).
- CATVariant: 97 out of 100 (learned from overlapping clinical labels, so this is optimistic)
- MetaLR: 94 out of 100 (learned from overlapping clinical labels, so this is optimistic)
- PolyPhen-2: 94 out of 100 (learned from overlapping clinical labels, so this is optimistic)
- SIFT: 88 out of 100
Diseases related to Anophthalmia/microphthalmia-esophageal atresia syndrome
- Jackson-Weiss syndrome, also linked to SOX2
- Developmental disorder, also linked to SOX2
Frequently asked questions
Which genes are linked to Anophthalmia/microphthalmia-esophageal atresia syndrome?
In CATVariant, Anophthalmia/microphthalmia-esophageal atresia syndrome is linked to 1 analyzed protein: SOX2 (Transcription factor SOX-2).
How many genetic variants are linked to Anophthalmia/microphthalmia-esophageal atresia syndrome?
86 variants: 13 are classified as disease-causing (pathogenic or likely pathogenic) in ClinVar and 31 are of uncertain significance or have conflicting reports.
Which uncertain variants in Anophthalmia/microphthalmia-esophageal atresia syndrome look disease-causing?
None of the uncertain variants currently reaches the likely-pathogenic range on computable evidence alone.
Which variant effect predictor works best for Anophthalmia/microphthalmia-esophageal atresia syndrome?
Among tools not trained on clinical labels, SIFT separates this disease's known disease-causing variants from harmless ones best (AUROC 0.88, based on 11 disease-causing and 11 harmless variants).
About this data
Variant–disease links come from ClinVar, Open Targets and UniProt, pooled from the latest public CATVariant analysis of each human protein. Evidence scores use the ACMG/AMP Bayesian points scale with computable criteria only (position among known disease variants, rarity in gnomAD, calibrated predictors, deep mutational scanning); there is no family or patient data, so they prioritise variants for expert review and never classify them.
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