Is OCLN p.Ile79= (c.237C>T) pathogenic?

OCLN p.Ile79= (c.237C>T) is classified Likely benign in OCLN (ClinVar, Single submitter, 1 submitter; last evaluated 2016-03-30). Absent from gnomAD v4.1.

How common is OCLN p.Ile79= (c.237C>T) in the general population?

OCLN p.Ile79= (c.237C>T) is absent from gnomAD v4.1 (gnomAD).

OCLN p.Ile79=

c.237C>T · rs1057522081 · VCV384939

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 -0.32	phastCons 0.004
Overall
CADD	2.604	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: OCLN
Protein: p.Ile79=
Coding: c.237C>T
MANE Select: NM_001205254
dbSNP: rs1057522081
Type: single nucleotide variant
Location: chr5:69509327 (GRCh38)
Gene constraint: LOEUF 0.728 · pLI 0.02 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 65.82 · 3 PDB
Residue 79: the marvel domain

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

Similar variants

OCLN c.1037+1G>A Pathogenic/Likely pathogenic ★★ same type
OCLN p.Arg36Ter Pathogenic ★★ same type
OCLN p.Ala152Thr Uncertain significance ★★ ⚠ same type
OCLN p.Arg66Leu Uncertain significance ★★ ⚠ same type
OCLN p.Gln211Lys Uncertain significance ★★ ⚠ same type
OCLN p.Gln41Glu Uncertain significance ★★ ⚠ same type
OCLN p.Ile212Val Uncertain significance ★★ ⚠ same type
OCLN p.Met70Val Uncertain significance ★★ ⚠ 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/ocln-p-ile79 (accessed [today's date]).

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