OCLN p.Ser370=
c.1110C>T · VCV4970642
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00228%, eas)
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 1.4 | phastCons 0.96 |
| Overall | ||
| CADD | 14.4 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00228%
East Asian · 1/43,856 alleles
Filtering AF
0.000364%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000264%
Overall
0.000758%
12/1,583,058 alleles · very rare
exomes 10/1,450,116 · genomes 2/132,942 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00228% | 43,856 |
| Admixed American | 0.00174% | 57,332 |
| Remaining individualsnot grpmax-eligible | 0.00162% | 61,736 |
| European (non-Finnish) | 0.000774% | 129,144 |
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.Ser370=
- Coding
- c.1110C>T
- MANE Select
- NM_001205254
- Type
- single nucleotide variant
- Location
- chr5:69544976 (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 370
- the 'disordered' region; a modified residue (phosphoserine)
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-ser370 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown