ATOH7 p.Pro125=
c.375G>C · rs767426217 · VCV1123106
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0667%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>T here scores Δ0.30 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -7.7 | GERP -5.1 |
| Overall | ||
| CADD | 4.832 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0667%
Middle Eastern · 4/5,996 alleles
Filtering AF
0.0275%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0241%
Overall
0.00329%
53/1,611,608 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0667% | 1,499 |
| South Asian | 0.0374% | 2,672 |
| East Asian | 0.00447% | 22,350 |
| Admixed American | 0.00167% | 59,820 |
| Finnishnot grpmax-eligible | 0.00158% | 63,326 |
| European (non-Finnish) | 0.000933% | 107,208 |
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
- ATOH7
- Protein
- p.Pro125=
- Coding
- c.375G>C
- MANE Select
- NM_145178
- dbSNP
- rs767426217
- Type
- single nucleotide variant
- Location
- chr10:68231303 (GRCh38)
- Gene constraint
- LOEUF 1.758 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 72.79
Similar variants
- ATOH7 p.Ala20Gly Uncertain significance ★★ ⚠ same type
- ATOH7 p.Ala20Thr Uncertain significance ★★ ⚠ same type
- ATOH7 p.Ala44Glu Uncertain significance ★★ ⚠ same type
- ATOH7 p.Ala59Val Uncertain significance ★★ ⚠ same type
- ATOH7 p.Arg62Ser Uncertain significance ★★ ⚠ same type
- ATOH7 p.Arg94Trp Uncertain significance ★★ same type
- ATOH7 p.Asn46Ser Uncertain significance ★★ ⚠ same type
- ATOH7 p.Asn57Ser 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/atoh7-p-pro125 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown