OTOG p.Pro989=
c.2967G>A · rs11024331 · VCV226877
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 6 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.25%, 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 -14 | GERP -5.3 |
| Overall | ||
| CADD | 4.549 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.25%
African / African-American · 918/73,176 alleles
Filtering AF
1.19%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.16%
Overall
0.0669%
1,037/1,550,632 alleles · low-frequency
exomes 492/1,398,300 · genomes 545/152,332 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.25% | 80 |
| Admixed American | 0.118% | 850 |
| Remaining individualsnot grpmax-eligible | 0.0649% | 1,541 |
| Middle Eastern | 0.0334% | 2,996 |
| East Asian | 0.00489% | 20,462 |
| European (non-Finnish) | 0.00131% | 76,468 |
| South Asian | 0.00119% | 84,064 |
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.Pro989=
- Coding
- c.2967G>A
- MANE Select
- NM_001292063
- dbSNP
- rs11024331
- Type
- single nucleotide variant
- Location
- chr11:17591549 (GRCh38)
- Gene constraint
- LOEUF 1.091 · pLI <0.01 (gnomAD)
- Residue 989
- the vwfd 3 domain
Similar variants
- OTOG p.Pro989Leu Uncertain significance ★★ ⚠ same residue
- 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
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-pro989 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown