Is OCA2 p.Ser788= (c.2364G>A) pathogenic?

OCA2 p.Ser788= (c.2364G>A) is classified Benign in OCA2 (ClinVar, Multiple submitters, 8 submitters; last evaluated 2026-02-04). Common (popmax 58.4%, eas) — too common for a highly-penetrant pathogenic allele; Associated with oculocutaneous albinism type 2.

What condition is associated with OCA2 p.Ser788= (c.2364G>A)?

OCA2 p.Ser788= (c.2364G>A) is associated with oculocutaneous albinism type 2 (ClinVar).

How is Oculocutaneous albinism type 2 inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

OCA2 p.Ser788=

Q: How common is OCA2 p.Ser788= (c.2364G>A) in the general population?

OCA2 p.Ser788= (c.2364G>A) is common (popmax 58.4%, eas) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.2364G>A · rs12592307 · VCV255730

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 8 submitters

gnomAD v4.1

Common

common (popmax 58.4%, eas) — too common for a highly-penetrant pathogenic allele

Conditions

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 -6.9	GERP -4.6
Overall
CADD	0.114	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 58.4% East Asian · 26,167/44,838 alleles

Filtering AF 57.8% ClinGen BA1/BS1 input FAF95, joint · FAF99 57.5%

Overall 22.2% 357,452/1,612,506 alleles · common exomes 325,647/1,460,688 · genomes 31,805/151,818 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	58.4%	2
Amishnot grpmax-eligible	42.4%	2
Admixed American	40.9%	2
Ashkenazi Jewishnot grpmax-eligible	32.3%	3
South Asian	31.2%	3
Middle Eastern	26.6%	4
Remaining individualsnot grpmax-eligible	23.9%	4
Finnishnot grpmax-eligible	23.5%	4
European (non-Finnish)	19.4%	5
African / African-American	10.6%	9

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.Ser788=
Coding: c.2364G>A
MANE Select: NM_000275
dbSNP: rs12592307
Type: single nucleotide variant
Location: chr15:27845027 (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 type 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Oculocutaneous albinism type 2 (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal
Prevalence: 6-9 / 10 000 (Specific population)

Similar variants

OCA2 p.Ser788Leu Pathogenic/Likely pathogenic ★★ 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-ser788 (accessed [today's date]).

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