OCA2 p.Ala480=
c.1440T>C · rs2548339162 · VCV2830054
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.3 | GERP -3.2 |
| Overall | ||
| CADD | 4.356 | 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
- OCA2
- Protein
- p.Ala480=
- Coding
- c.1440T>C
- MANE Select
- NM_000275
- dbSNP
- rs2548339162
- Type
- single nucleotide variant
- Location
- chr15:27983408 (GRCh38)
- Gene constraint
- LOEUF 0.869 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 73.79
Similar variants
- OCA2 p.Ala480Pro Uncertain significance ★ ⚠ same residue
- OCA2 p.Ala480fs Pathogenic ★ same residue
- OCA2 c.1044+1G>T Pathogenic ★★ same type
- OCA2 c.1044+2T>C Pathogenic/Likely pathogenic ★★ same type
- OCA2 c.1045-15T>G Pathogenic/Likely pathogenic ★★ same type
- OCA2 c.1116+2T>C Likely pathogenic ★★ same type
- OCA2 c.1182+1G>A Pathogenic ★★ same type
- OCA2 c.1239+2T>A Likely pathogenic ★★ same type
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-ala480 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown