OCRL c.2139+7C>T
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000563%, nfe)
Conditions
1
oculocerebrorenal syndrome
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +7 | near-intronic (+7 nt from the splice site) · inside the BP7-excluded zone |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.4 | GERP -1, phastCons 0.74 |
| Non-coding constraint | — | not assessed · autosomes only, so chrX has no window · absence ≠ unconstrained |
| Overall | ||
| CADD | 9.917 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000563%
European (non-Finnish) · 5/888,702 alleles
Filtering AF
0.000165%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00012%
Overall
0.000415%
5/1,204,298 alleles · very rare
exomes 5/1,090,704 · genomes 0/113,594 · 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
- Coding
- c.2139+7C>T
- MANE Select
- NM_000276
- dbSNP
- rs1331551611
- Type
- single nucleotide variant
- Location
- chrX:129584374 (GRCh38)
- Structure
- AlphaFold pLDDT 82.91 · 5 PDB
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-c-2139-plus-7c-t (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown