OGFR p.Pro586=
c.1758G>A · rs74520364 · VCV2652503
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00234%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -4.6 | GERP -0.68 |
| Overall | ||
| CADD | 5.932 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00234%
East Asian · 1/42,736 alleles
Filtering AF
8.1e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5.5e-05%
Overall
0.000389%
6/1,543,478 alleles · very rare
exomes 4/1,424,564 · genomes 2/118,914 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00234% | 42,736 |
| Finnishnot grpmax-eligible | 0.00202% | 49,506 |
| European (non-Finnish) | 0.000346% | 289,006 |
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
- OGFR
- Protein
- p.Pro586=
- Coding
- c.1758G>A
- MANE Select
- NM_007346
- dbSNP
- rs74520364
- Type
- single nucleotide variant
- Location
- chr20:62813373 (GRCh38)
- Gene constraint
- LOEUF 0.984 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 63.00
- Residue 586
- the 'disordered' region; the '7 x 20 aa approximate tandem repeats of [st]-p-s-e-t-p-g-p-[sr]-p-a-g-p-[at]-[gr]-d-e-p-a-[ek]' region
Similar variants
- OGFR p.Ala253Val Uncertain significance ★ ⚠ same type
- OGFR p.Ala411Thr Uncertain significance ★ ⚠ same type
- OGFR p.Ala469Thr Uncertain significance ★ ⚠ same type
- OGFR p.Ala480Val Uncertain significance ★ ⚠ same type
- OGFR p.Ala627Val Uncertain significance ★ ⚠ same type
- OGFR p.Ala655Thr Uncertain significance ★ ⚠ same type
- OGFR p.Ala660Val Uncertain significance ★ ⚠ same type
- OGFR p.Arg138Gln 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/ogfr-p-pro586 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown