OCRL p.Pro407=
c.1221G>A · rs747651906 · VCV588931
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.023%, mid)
Conditions
1
oculocerebrorenal syndrome
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 -2.8 | GERP -5.5 |
| Overall | ||
| CADD | 0.207 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.023%
Middle Eastern · 1/4,349 alleles
Filtering AF
0.00571%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00408%
Overall
0.00579%
70/1,209,300 alleles · ultra-rare
exomes 56/1,097,677 · genomes 14/111,623 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.023% | 4,349 |
| South Asian | 0.0123% | 8,111 |
| African / African-American | 0.00876% | 11,422 |
| Admixed American | 0.00656% | 15,233 |
| Remaining individualsnot grpmax-eligible | 0.00631% | 15,860 |
| European (non-Finnish) | 0.00559% | 17,896 |
| East Asian | 0.00296% | 33,753 |
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
- OCRL
- Protein
- p.Pro407=
- Coding
- c.1221G>A
- MANE Select
- NM_000276
- dbSNP
- rs747651906
- Type
- single nucleotide variant
- Location
- chrX:129562763 (GRCh38)
- Structure
- AlphaFold pLDDT 82.91 · 5 PDB
- Residue 407
- the 5-ppase domain
Similar variants
- OCRL p.Pro407Arg Uncertain significance ★ ⚠ same residue
- OCRL p.Pro407Leu Uncertain significance ★ ⚠ same residue
- OCRL c.1244+1G>A Pathogenic/Likely pathogenic ★★ same condition
- OCRL c.1714-1G>A Pathogenic ★★ same condition
- OCRL c.2256+1G>T Likely pathogenic ★★ same condition
- OCRL c.560+1G>C Pathogenic/Likely pathogenic ★★ same condition
- OCRL c.940-11G>A Pathogenic/Likely pathogenic ★★ same condition
- OCRL p.Ala861Thr Pathogenic/Likely 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/ocrl-p-pro407 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown