Is OPA1 p.Phe802fs (c.2406del) pathogenic?

OPA1 p.Phe802fs (c.2406del) is classified Pathogenic in OPA1 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2024-10-11). No gnomAD frequency available for this variant; Associated with OPA1-related disorder.

What condition is associated with OPA1 p.Phe802fs (c.2406del)?

OPA1 p.Phe802fs (c.2406del) is associated with OPA1-related disorder, autosomal dominant optic atrophy, classic form (ClinVar).

How common is OPA1 p.Phe802fs (c.2406del) in the general population?

OPA1 p.Phe802fs (c.2406del) is no gnomAD frequency available for this variant (gnomAD).

OPA1 p.Phe802fs

c.2406del · rs1553785025 · VCV447898

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

OPA1-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a LoF-intolerant gene
NMD	predicted	premature termination codon in exon 24 of 31
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 5.3	GERP -0.071, 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: OPA1
Protein: p.Phe802fs
Coding: c.2406del
MANE Select: NM_130837
dbSNP: rs1553785025
Type: Deletion
Location: chr3:193658958 (GRCh38)
Gene constraint: LOEUF 0.503 · pLI 0.92 (gnomAD)
Structure: AlphaFold pLDDT 74.02 · 11 PDB
Residue 802: the 'stalk region' region; the 'paddle region' region

Full OPA1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

OPA1-related disorder

Also linked: autosomal dominant optic atrophy, classic form

Similar variants

OPA1 c.1377_1377+4del Pathogenic/Likely pathogenic ★★ same condition
OPA1 c.2012+4_2012+7del Pathogenic/Likely pathogenic ★★ same condition
OPA1 c.2873_2876del Pathogenic/Likely pathogenic ★★ same condition
OPA1 p.Gln714fs Likely pathogenic ★★ same condition
OPA1 p.Lys267fs Pathogenic ★★ same condition
OPA1 p.Phe772fs Pathogenic/Likely pathogenic ★★ same condition
OPA1 p.Ser763fs Pathogenic ★★ same condition
OPA1 p.Tyr113fs 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/opa1-p-phe802fs (accessed [today's date]).

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