ATOH7 p.Pro68=
c.204C>T · rs140546531 · VCV1168752
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.126%, sas)
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 -3.3 | GERP -5.6 |
| Overall | ||
| CADD | 1.829 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.126%
South Asian · 113/89,796 alleles
Filtering AF
0.107%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0999%
Overall
0.00761%
122/1,602,118 alleles · rare
exomes 116/1,449,902 · genomes 6/152,216 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.126% | 795 |
| Remaining individualsnot grpmax-eligible | 0.00484% | 20,669 |
| Admixed American | 0.00341% | 29,363 |
| European (non-Finnish) | 0.000341% | 293,671 |
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.Pro68=
- Coding
- c.204C>T
- MANE Select
- NM_145178
- dbSNP
- rs140546531
- Type
- single nucleotide variant
- Location
- chr10:68231474 (GRCh38)
- Gene constraint
- LOEUF 1.758 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 72.79
- Residue 68
- the bhlh domain
Similar variants
- ATOH7 p.Pro68Ala Uncertain significance ★ ⚠ same residue
- ATOH7 p.Pro68Arg Uncertain significance ★ ⚠ same residue
- ATOH7 p.Pro68Ser Uncertain significance ★ ⚠ same residue
- 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
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-pro68 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown