OTOG p.Ser79=
c.237C>T · rs11823045 · VCV226872
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 6 submitters
gnomAD v4.1
Common
common (popmax 29.7%, afr) — too common for a highly-penetrant pathogenic allele
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 -0.46 | GERP -2.5 |
| Overall | ||
| CADD | 6.452 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
29.7%
African / African-American · 21,695/73,068 alleles
Filtering AF
29.4%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 29.2%
Overall
2.93%
45,455/1,550,372 alleles · common
exomes 31,308/1,398,168 · genomes 14,147/152,204 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 29.7% | 3 |
| Middle Eastern | 5.62% | 18 |
| Ashkenazi Jewishnot grpmax-eligible | 4.96% | 20 |
| Remaining individualsnot grpmax-eligible | 3.84% | 26 |
| Admixed American | 2.74% | 36 |
| European (non-Finnish) | 1.47% | 68 |
| South Asian | 1.36% | 73 |
| Finnishnot grpmax-eligible | 0.491% | 204 |
| Amishnot grpmax-eligible | 0.329% | 304 |
| East Asian | 0.00489% | 20,458 |
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
- OTOG
- Protein
- p.Ser79=
- Coding
- c.237C>T
- MANE Select
- NM_001292063
- dbSNP
- rs11823045
- Type
- single nucleotide variant
- Location
- chr11:17552020 (GRCh38)
- Gene constraint
- LOEUF 1.091 · pLI <0.01 (gnomAD)
Similar variants
- OTOG c.6934-2A>G Likely pathogenic ★★ same type
- OTOG c.996+1G>T Pathogenic ★★ same type
- OTOG p.Arg1063Ter Pathogenic/Likely pathogenic ★★ same type
- OTOG p.Arg1153Ter Pathogenic/Likely pathogenic ★★ same type
- OTOG p.Arg1222Ter Pathogenic/Likely pathogenic ★★ same type
- OTOG p.Arg1903Ter Pathogenic/Likely pathogenic ★★ same type
- OTOG p.Arg2175Ter Pathogenic/Likely pathogenic ★★ same type
- OTOG p.Arg2473Ter Pathogenic/Likely pathogenic ★★ 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/otog-p-ser79 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown