OCRL p.Phe463=
c.1389T>C · rs2521901712 · VCV2955095
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00176%, sas)
Conditions
1
oculocerebrorenal syndrome
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 3.4 | GERP 0.48, phastCons 1 |
| Overall | ||
| CADD | 8.948 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00176%
South Asian · 1/56,909 alleles
Overall
8.27e-05%
1/1,209,394 alleles · very rare
exomes 1/1,095,466 · genomes 0/113,928 · 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
- OCRL
- Protein
- p.Phe463=
- Coding
- c.1389T>C
- MANE Select
- NM_000276
- dbSNP
- rs2521901712
- Type
- single nucleotide variant
- Location
- chrX:129567286 (GRCh38)
- Structure
- AlphaFold pLDDT 82.91 · 5 PDB
- Residue 463
- the 5-ppase domain; a UniProt-annotated variant site (in ocrl); a β-strand
Similar variants
- 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
- OCRL p.Arg318Cys Pathogenic/Likely pathogenic ★★ same condition
- OCRL p.Arg318His 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-phe463 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown