Is ATOH7 p.Ala16= (c.48A>G) pathogenic?

ATOH7 p.Ala16= (c.48A>G) is classified Likely benign in ATOH7 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-10-05). Very rare (popmax 0.00162%, afr).

How common is ATOH7 p.Ala16= (c.48A>G) in the general population?

ATOH7 p.Ala16= (c.48A>G) is very rare (popmax 0.00162%, afr) (gnomAD).

ATOH7 p.Ala16=

c.48A>G · rs1013711090 · VCV1080757

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00162%, afr)

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 -0.31	GERP -4.7
Overall
CADD	7.441	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00162% African / African-American · 1/61,780 alleles

Overall 0.000666% 1/150,164 alleles · very rare

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.Ala16=
Coding: c.48A>G
MANE Select: NM_145178
dbSNP: rs1013711090
Type: single nucleotide variant
Location: chr10:68231630 (GRCh38)
Gene constraint: LOEUF 1.758 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 72.79

Full ATOH7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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-ala16 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown