OCRL p.Ser648=
c.1944G>A · rs776881376 · VCV1299822
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0123%, sas)
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 -2.6 | GERP -5.4 |
| Overall | ||
| CADD | 0.148 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0123%
South Asian · 7/56,789 alleles
Filtering AF
0.00571%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00408%
Overall
0.0024%
29/1,209,369 alleles · ultra-rare
exomes 27/1,097,575 · genomes 2/111,794 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0123% | 8,113 |
| African / African-American | 0.0035% | 28,593 |
| European (non-Finnish) | 0.00224% | 44,734 |
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.Ser648=
- Coding
- c.1944G>A
- MANE Select
- NM_000276
- dbSNP
- rs776881376
- Type
- single nucleotide variant
- Location
- chrX:129576381 (GRCh38)
- Structure
- AlphaFold pLDDT 82.91 · 5 PDB
- Residue 648
- an α-helix; the 'ash' region
Similar variants
- OCRL p.Ser648Leu 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
- OCRL p.Arg318Cys 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-ser648 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown