Is OCA2 p.Ser289fs (c.867del) pathogenic?

OCA2 p.Ser289fs (c.867del) is classified Pathogenic in OCA2 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-03-28). No gnomAD frequency available for this variant; Associated with oculocutaneous albinism type 2.

What condition is associated with OCA2 p.Ser289fs (c.867del)?

OCA2 p.Ser289fs (c.867del) is associated with oculocutaneous albinism type 2 (ClinVar).

How common is OCA2 p.Ser289fs (c.867del) in the general population?

OCA2 p.Ser289fs (c.867del) is no gnomAD frequency available for this variant (gnomAD).

How is Oculocutaneous albinism type 2 inherited?

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

OCA2 p.Ser289fs

c.867del · rs794727898 · VCV198706

Pathogenic Multiple submitters

Classification

Pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

oculocutaneous albinism type 2

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 8 of 24
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 2.9	GERP 1.6, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: OCA2
Protein: p.Ser289fs
Coding: c.867del
MANE Select: NM_000275
dbSNP: rs794727898
Type: Deletion
Location: chr15:28016127 (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.Ala696fs Pathogenic/Likely pathogenic ★★ same condition
OCA2 p.Arg137fs Pathogenic ★★ same condition
OCA2 p.Arg53fs Pathogenic/Likely pathogenic ★★ same condition
OCA2 p.Asn603fs Pathogenic/Likely pathogenic ★★ same condition
OCA2 p.Glu253fs Pathogenic ★★ same condition
OCA2 p.Gly44fs Pathogenic/Likely pathogenic ★★ same condition
OCA2 p.Leu207_Leu212del Pathogenic/Likely pathogenic ★★ same condition
OCA2 p.Leu316_Leu317insTer 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-ser289fs (accessed [today's date]).

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