OCA2 p.Glu693=
c.2079G>A · rs1374558186 · VCV623862
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0107%, afr)
Conditions
1
OCA2-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.89 | donor loss at this position · masked 0 · deltas |
|---|---|---|
| Pangolin | Δ0.60 | loss · gain 0.01 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 7.5 | phastCons 1 |
| Overall | ||
| CADD | 20.3 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0107%
African / African-American · 8/74,908 alleles
Filtering AF
0.00528%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00381%
Overall
0.000496%
8/1,613,894 alleles · ultra-rare
exomes 6/1,461,752 · genomes 2/152,142 · joint denominator
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- OCA2
- Protein
- p.Glu693=
- Coding
- c.2079G>A
- MANE Select
- NM_000275
- dbSNP
- rs1374558186
- Type
- single nucleotide variant
- Location
- chr15:27926127 (GRCh38)
- Gene constraint
- LOEUF 0.869 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 73.79
Disease context
OCA2-related disorder
Similar variants
- OCA2 p.Glu693Val Uncertain significance ★ ⚠ same residue
- OCA2 c.1044+1G>T Pathogenic ★★ same condition
- OCA2 c.1044+2T>C Pathogenic/Likely pathogenic ★★ same condition
- OCA2 c.1045-15T>G Pathogenic/Likely pathogenic ★★ same condition
- OCA2 c.1239+2T>A Likely pathogenic ★★ same condition
- OCA2 c.1503+5G>A Pathogenic/Likely pathogenic ★★ same condition
- OCA2 c.1504-2A>G Pathogenic/Likely pathogenic ★★ same condition
- OCA2 c.1784+1G>A Pathogenic/Likely 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/oca2-p-glu693 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown