OCLN p.Pro19=
c.57G>A · rs370812139 · VCV2878760
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0022%, sas)
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 -0.51 | GERP -5.1, phastCons 0.003 |
| Overall | ||
| CADD | 8.035 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0022%
South Asian · 2/91,068 alleles
Filtering AF
0.000365%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000137%
Overall
0.000372%
6/1,613,664 alleles · very rare
exomes 6/1,461,386 · genomes 0/152,278 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0022% | 45,534 |
| European (non-Finnish) | 0.000339% | 294,906 |
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
- OCLN
- Protein
- p.Pro19=
- Coding
- c.57G>A
- MANE Select
- NM_001205254
- dbSNP
- rs370812139
- Type
- single nucleotide variant
- Location
- chr5:69509147 (GRCh38)
- Gene constraint
- LOEUF 0.728 · pLI 0.02 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 65.82 · 3 PDB
- Residue 19
- the 'disordered' region
Similar variants
- OCLN c.1037+1G>A Pathogenic/Likely pathogenic ★★ same type
- OCLN p.Arg36Ter Pathogenic ★★ same type
- OCLN p.Ala152Thr Uncertain significance ★★ ⚠ same type
- OCLN p.Arg66Leu Uncertain significance ★★ ⚠ same type
- OCLN p.Gln211Lys Uncertain significance ★★ ⚠ same type
- OCLN p.Gln41Glu Uncertain significance ★★ ⚠ same type
- OCLN p.Ile212Val Uncertain significance ★★ ⚠ same type
- OCLN p.Met70Val 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/ocln-p-pro19 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown