MYO7A p.Ala104=
c.312T>C · rs782654142 · VCV2787209
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00111%, 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 -7.2 | GERP -3.5 |
| Overall | ||
| CADD | 0.501 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00111%
South Asian · 1/90,110 alleles
Overall
6.21e-05%
1/1,609,174 alleles · very rare
exomes 1/1,456,808 · genomes 0/152,366 · 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
- MYO7A
- Protein
- p.Ala104=
- Coding
- c.312T>C
- MANE Select
- NM_000260
- dbSNP
- rs782654142
- Type
- single nucleotide variant
- Location
- chr11:77155933 (GRCh38)
- Gene constraint
- LOEUF 0.995 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.73 · 1 PDB
- Residue 104
- the myosin motor domain
Similar variants
- MYO7A p.Ala104Thr Conflicting classifications of pathogenicity ★ ⚠ same residue
- MYO7A p.Ala104_Val105insTer Likely pathogenic same residue
- MYO7A p.Ala1288Pro Likely pathogenic ★★★ same type
- MYO7A p.Arg1168Gln Pathogenic ★★★ ⚠ same type
- MYO7A p.Arg1873Gln Pathogenic ★★★ ⚠ same type
- MYO7A p.Arg395Cys Likely pathogenic ★★★ ⚠ same type
- MYO7A p.Arg668Cys Pathogenic ★★★ same type
- MYO7A p.Arg853His Likely pathogenic ★★★ 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/myo7a-p-ala104 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown