OTX2 p.Pro39=
c.117C>G · rs1762201449 · VCV3036051
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
OTX2-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.47 | acceptor gain, 19 bp away · masked 0 · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.7 | GERP 0.53, phastCons 1 |
| Overall | ||
| CADD | 19.8 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- OTX2
- Protein
- p.Pro39=
- Coding
- c.117C>G
- MANE Select
- NM_021728
- dbSNP
- rs1762201449
- Type
- single nucleotide variant
- Location
- chr14:56804344 (GRCh38)
- Gene constraint
- LOEUF 0.324 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 60.99
- Residue 39
- a DNA-binding region
Disease context
OTX2-related disorder
Similar variants
- OTX2 p.Glu87Lys Pathogenic/Likely pathogenic ★★ same condition
- OTX2 p.Tyr197Ter Pathogenic/Likely pathogenic ★★ same condition
- OTX2 p.Pro141Ser Uncertain significance ★★ ⚠ same condition
- OTX2 p.Arg47fs Likely pathogenic ★ same condition
- OTX2 p.Ile159fs Pathogenic ★ same condition
- OTX2 p.Ile83fs Likely pathogenic ★ same condition
- OTX2 p.Lys45fs Likely pathogenic ★ same condition
- OTX2 p.Phe204fs Pathogenic ★ same condition
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/otx2-p-pro39 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown