ATOH7 p.Arg65=
c.193A>C · rs111699024 · VCV1918329
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00547%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.39 | acceptor loss, 2 bp away · masked 0 · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.5 | GERP -5.2 |
| Overall | ||
| CADD | 8.979 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00547%
African / African-American · 4/73,140 alleles
Filtering AF
0.00178%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00106%
Overall
0.000689%
11/1,595,922 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00547% | 18,285 |
| Admixed American | 0.00345% | 29,001 |
| Remaining individualsnot grpmax-eligible | 0.00324% | 30,829 |
| European (non-Finnish) | 0.000256% | 390,549 |
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.Arg65=
- Coding
- c.193A>C
- MANE Select
- NM_145178
- dbSNP
- rs111699024
- Type
- single nucleotide variant
- Location
- chr10:68231485 (GRCh38)
- Gene constraint
- LOEUF 1.758 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 72.79
- Residue 65
- the bhlh domain; a UniProt-annotated variant site (does not affect dna-binding activity or transcription activation)
Similar variants
- ATOH7 p.Arg65Gly Benign ★★ 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
- ATOH7 p.Arg94Trp Uncertain significance ★★ same type
- ATOH7 p.Asn46Ser 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-arg65 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown