OTOGL p.Val1007Phe
c.3019G>T · VCV3926720
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00823%, sas)
Conditions
1
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.277 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.5 | GERP -0.2, phastCons 0.84 |
| Regional constraint | o/e 1.03 | unconstrained · MANE · 157 kb · p 0.1 · regional, not allelic |
| Overall | ||
| CADD | 19.11 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00823%
South Asian · 7/85,048 alleles
Filtering AF
0.00381%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00269%
Overall
0.000451%
7/1,550,658 alleles · very rare
exomes 7/1,398,348 · genomes 0/152,310 · joint denominator
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
- OTOGL
- Protein
- p.Val1007Phe
- Coding
- c.3019G>T
- MANE Select
- NM_001378609
- Type
- single nucleotide variant
- Location
- chr12:80296917 (GRCh38)
- Gene constraint
- LOEUF 1.069 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 72.19
- Residue 1007
- the vwfd 3 domain
Similar variants
- OTOGL p.Val1007Ala Likely benign ★★ same residue
- OTOGL c.3213+1G>A Likely pathogenic ★★ same condition
- OTOGL p.Arg1515Ter Pathogenic/Likely pathogenic ★★ same condition
- OTOGL p.Trp647Ter Pathogenic/Likely pathogenic ★★ same condition
- OTOGL p.Ala1270Glu Uncertain significance ★★ same condition
- OTOGL p.Ala1299Val Uncertain significance ★★ same condition
- OTOGL p.Ala280Thr Uncertain significance ★★ same condition
- OTOGL p.Ala644Thr Uncertain significance ★★ same condition
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/otogl-p-val1007phe (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown