Anophthalmia/microphthalmia - esophageal atresia: genes and variants
Explore variant evidence for Anophthalmia/microphthalmia - esophageal atresia across 1 analyzed protein (SOX2). Linked ClinVar records include 13 pathogenic or likely pathogenic variants, 24 variants of uncertain significance and 7 with conflicting classifications.
Coverage includes proteins already analyzed in CATVariant, not every gene involved in this condition. Database links are associations, not an assessment of clinical gene–disease validity. Computable evidence prioritizes variants for expert review and does not reclassify them. Source labels are pooled across this disease family.
Data updated 2026-10-10. Automated aggregation, not a clinical review date.
Download variant evidence (CSV)
Genes linked to Anophthalmia/microphthalmia - esophageal atresia
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 ClinVar pathogenic / likely pathogenic and 31 uncertain variants in SOX2 have source records linked to Anophthalmia/microphthalmia - esophageal atresia. Association strength is not clinical gene validity.
Where Anophthalmia/microphthalmia - esophageal atresia variants cluster
- SOX2 HMG box (positions 41–109): 9 of 13 ClinVar pathogenic / likely pathogenic variants, 3.2× more than its size predicts.
ClinVar pathogenic and likely pathogenic variants linked to Anophthalmia/microphthalmia - esophageal atresia
| Variant | Position | Protein part | Clinical label |
|---|---|---|---|
| SOX2 P112L | 112 | Pathogenic / likely pathogenic (★★) | |
| SOX2 F48S | 48 | HMG box | Pathogenic / likely pathogenic (★) |
| SOX2 F48V | 48 | HMG box | Pathogenic / likely pathogenic (★) |
| SOX2 R96P | 96 | HMG box | Pathogenic / likely pathogenic (★) |
| SOX2 Y110S | 110 | Pathogenic / likely pathogenic (★) | |
| SOX2 R113W | 113 | Pathogenic / likely pathogenic (★) | |
| SOX2 A287P | 287 | Pathogenic / likely pathogenic (★) | |
| SOX2 N46K | 46 | HMG box | Pathogenic / likely pathogenic |
| SOX2 L97P | 97 | HMG box | Pathogenic / likely pathogenic |
| SOX2 R98P | 98 | HMG box | Pathogenic / likely pathogenic |
| SOX2 P44R | 44 | HMG box | Pathogenic / likely pathogenic |
| SOX2 R56G | 56 | HMG box | Pathogenic / likely pathogenic |
| SOX2 R74P | 74 | HMG box | Pathogenic / likely pathogenic |
Which prediction tools work for Anophthalmia/microphthalmia - esophageal atresia
Observed separation of ClinVar pathogenic / likely pathogenic from benign / likely benign variants (AUROC × 100). This benchmark is not a clinical recommendation.
- 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
- Jackson-Weiss syndrome, also linked to SOX2
- Developmental disorder, also linked to SOX2
Frequently asked questions
Which genes have records linked to Anophthalmia/microphthalmia - esophageal atresia?
This view contains 1 analyzed proteins: SOX2. Links come from clinical records and association databases. They do not imply that every listed gene is a validated cause, and missing genes may not yet be analyzed.
What do the clinical classifications mean?
Linked records include 13 pathogenic or likely pathogenic variants, 24 variants of uncertain significance and 7 with conflicting classifications. Labels summarize source records; multi-condition records may not make a separate assertion for this disease. Check the original record and review status.
Does the evidence score change a VUS classification?
No. 0 VUS or conflicting variants reach the likely-pathogenic points range on the computable criteria available here. This is a research prioritization signal, not a clinical classification. Patient, family and other required evidence may be missing.
Can I download the variant evidence?
Download the CSV for all 86 variants in the selected disease scope, including clinical labels, review status, evidence criteria, predictor scores, functional measurements and population frequency where available.
About this data
Variant–disease links come from ClinVar, Open Targets and UniProt, pooled from eligible public CATVariant analyses 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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