Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Common
common (popmax 5.31%, afr) — too common for a highly-penetrant pathogenic allele
Conditions
1
oculocutaneous albinism type 2
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 -20 | GERP -4.5 |
| Overall | ||
| CADD | 0.005 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
5.31%
African / African-American · 3,983/74,964 alleles
Filtering AF
5.18%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5.12%
Overall
0.388%
6,265/1,613,988 alleles · common
exomes 3,816/1,461,820 · genomes 2,449/152,168 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 5.31% | 19 |
| Ashkenazi Jewishnot grpmax-eligible | 1.71% | 58 |
| Middle Eastern | 0.759% | 132 |
| Remaining individualsnot grpmax-eligible | 0.67% | 149 |
| Admixed American | 0.535% | 187 |
| European (non-Finnish) | 0.0823% | 1,215 |
| South Asian | 0.0176% | 5,692 |
| East Asian | 0.00446% | 22,432 |
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.Ser736=
- Coding
- c.2208G>A
- MANE Select
- NM_000275
- dbSNP
- rs1800418
- Type
- single nucleotide variant
- Location
- chr15:27871190 (GRCh38)
- Gene constraint
- LOEUF 0.869 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 73.79
- Residue 736
- a UniProt-annotated variant site (in oca2)
Disease context
oculocutaneous albinism type 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Oculocutaneous albinism type 2 (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Infancy, Neonatal
- Prevalence
- 6-9 / 10 000 (Specific population)
Similar variants
- OCA2 p.Ser736Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
- OCA2 c.1044+1G>T Pathogenic ★★ same condition
- OCA2 c.1045-15T>G Pathogenic/Likely pathogenic ★★ same condition
- OCA2 c.1182+1G>A Pathogenic ★★ same condition
- OCA2 c.1365-1G>A 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.1842+1G>T 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-ser736 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown