Is OCA2 p.Gly485Val (c.1454G>T) pathogenic?

OCA2 p.Gly485Val (c.1454G>T) is classified Likely pathogenic in OCA2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-06-11). AlphaMissense: likely pathogenic (0.9962); Very rare (popmax 0.00133%, afr); Associated with oculocutaneous albinism.

What condition is associated with OCA2 p.Gly485Val (c.1454G>T)?

OCA2 p.Gly485Val (c.1454G>T) is associated with oculocutaneous albinism (ClinVar).

How common is OCA2 p.Gly485Val (c.1454G>T) in the general population?

OCA2 p.Gly485Val (c.1454G>T) is very rare (popmax 0.00133%, afr) (gnomAD).

What do computational predictors say about OCA2 p.Gly485Val (c.1454G>T)?

AlphaMissense predicts likely pathogenic (score 0.9962) — an in-silico prediction, not a clinical call.

OCA2 p.Gly485Val

c.1454G>T · rs2041233118 · VCV2736163

Likely pathogenic Multiple submitters

Classification

Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely pathogenic

0.9962 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00133%, afr)

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

oculocutaneous albinism

Computational evidence

Protein change
AlphaMissense	0.9962	likely pathogenic ✓ concordant with ClinVar · top 1% in OCA2
REVEL	0.971	strongly pathogenic-leaning
SaProt	LLR -17.61	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 7.6	GERP 1.8, phastCons 1
Regional constraint	o/e 0.98	unconstrained · MANE · 326 kb · p 0.41 · regional, not allelic
Overall
CADD	29.2	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00133% African / African-American · 1/74,916 alleles

Overall 6.2e-05% 1/1,614,046 alleles · very rare exomes 0/1,461,890 · genomes 1/152,156 · 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.Gly485Val
Coding: c.1454G>T
MANE Select: NM_000275
dbSNP: rs2041233118
Type: single nucleotide variant
Location: chr15:27983394 (GRCh38)
Gene constraint: LOEUF 0.869 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 73.79

Full OCA2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

oculocutaneous albinism — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

OCA2 p.Gly485Arg Pathogenic/Likely pathogenic ★★ same residue
OCA2 p.Gly485= Likely benign ★ same residue
OCA2 c.1842+1G>T Pathogenic/Likely pathogenic ★★ same condition
OCA2 p.Ala831Pro Pathogenic/Likely pathogenic ★★ same condition
OCA2 p.Arg136Ter Pathogenic ★★ same condition
OCA2 p.Asn476Asp Pathogenic ★★ same condition
OCA2 p.Asn476Ser Pathogenic/Likely pathogenic ★★ same condition
OCA2 p.Asn489Asp 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-gly485val (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown