OPA1 p.Asp307=
c.921C>T · rs147242797 · VCV381853
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
rare (popmax 0.103%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.419 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.8 | GERP -2.8, phastCons 1 |
| Overall | ||
| CADD | 9.732 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.103%
African / African-American · 77/74,822 alleles
Filtering AF
0.0843%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0776%
Overall
0.00536%
86/1,603,410 alleles · rare
exomes 44/1,451,204 · genomes 42/152,206 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.103% | 972 |
| Admixed American | 0.00834% | 11,996 |
| Remaining individualsnot grpmax-eligible | 0.00483% | 20,704 |
| South Asian | 0.0011% | 90,812 |
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
- OPA1
- Protein
- p.Asp307=
- Coding
- c.921C>T
- MANE Select
- NM_130837
- dbSNP
- rs147242797
- Type
- single nucleotide variant
- Location
- chr3:193635495 (GRCh38)
- Gene constraint
- LOEUF 0.503 · pLI 0.92 (gnomAD)
- Structure
- AlphaFold pLDDT 74.02 · 11 PDB
- Residue 307
- an α-helix; the dynamin-type g domain
Similar variants
- OPA1 c.1035+1G>A Pathogenic ★★ same type
- OPA1 c.1035+5G>A Pathogenic/Likely pathogenic ★★ same type
- OPA1 c.1149+1G>A Pathogenic ★★ same type
- OPA1 c.1149+1G>T Likely pathogenic ★★ same type
- OPA1 c.1150-2A>G Pathogenic ★★ same type
- OPA1 c.1230+1G>A Pathogenic ★★ same type
- OPA1 c.1230+5G>A Pathogenic/Likely pathogenic ★★ same type
- OPA1 c.1305+1G>T Pathogenic ★★ 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/opa1-p-asp307 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown