OPLAH p.Pro1069=
c.3207G>C · rs1835409083 · VCV3049937
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0011%, nfe)
Conditions
1
OPLAH-related disorder
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 -4.9 | GERP -3.2 |
| Overall | ||
| CADD | 0.641 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0011%
European (non-Finnish) · 13/1,177,008 alleles
Filtering AF
0.000616%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000475%
Overall
0.000815%
13/1,595,460 alleles · very rare
exomes 13/1,443,116 · genomes 0/152,344 · joint denominator
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
- OPLAH
- Protein
- p.Pro1069=
- Coding
- c.3207G>C
- MANE Select
- NM_017570
- dbSNP
- rs1835409083
- Type
- single nucleotide variant
- Location
- chr8:144052545 (GRCh38)
- Gene constraint
- LOEUF 1.163 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 88.08
Disease context
OPLAH-related disorder
Similar variants
- OPLAH p.Pro1069Arg Uncertain significance ★ ⚠ same residue
- OPLAH p.Gln950Ter Likely pathogenic same condition
- OPLAH c.1535+10G>A Likely benign same condition
- OPLAH p.Ala1073Val Likely benign ⚠ same condition
- OPLAH p.Val1087fs Likely pathogenic ★ same condition
- OPLAH p.Gly1015fs Likely pathogenic same condition
- OPLAH p.Pro1266fs Likely pathogenic same condition
- OPLAH c.587+1G>A Pathogenic/Likely 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/oplah-p-pro1069 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown