OTOG p.Ser178=
c.534C>T · rs61995706 · VCV504777
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 6 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.34%, afr)
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 -1.3 | GERP -5.5 |
| Overall | ||
| CADD | 5.049 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.34%
African / African-American · 935/69,570 alleles
Filtering AF
1.27%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.24%
Overall
0.0709%
1,018/1,435,582 alleles · low-frequency
exomes 482/1,283,276 · genomes 536/152,306 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.34% | 74 |
| Middle Eastern | 0.201% | 497 |
| Remaining individualsnot grpmax-eligible | 0.0836% | 1,197 |
| Admixed American | 0.0454% | 2,202 |
| South Asian | 0.00633% | 15,799 |
| European (non-Finnish) | 0.000641% | 156,069 |
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.Ser178=
- Coding
- c.534C>T
- MANE Select
- NM_001292063
- dbSNP
- rs61995706
- Type
- single nucleotide variant
- Location
- chr11:17553513 (GRCh38)
- Gene constraint
- LOEUF 1.091 · pLI <0.01 (gnomAD)
- Residue 178
- the vwfd 1 domain
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-ser178 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown