MYO7A p.Thr2001=
c.6003G>A · rs775879461 · VCV1011877
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00116%, sas)
Conditions
1
Usher syndrome type 1B
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 -16 | GERP -3.5 |
| Overall | ||
| CADD | 0.019 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00116%
South Asian · 1/86,190 alleles
Filtering AF
0.000549%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000434%
Overall
0.000821%
13/1,583,112 alleles · very rare
exomes 9/1,430,948 · genomes 4/152,164 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00116% | 86,190 |
| European (non-Finnish) | 0.00103% | 97,054 |
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.Thr2001=
- Coding
- c.6003G>A
- MANE Select
- NM_000260
- dbSNP
- rs775879461
- Type
- single nucleotide variant
- Location
- chr11:77208755 (GRCh38)
- Gene constraint
- LOEUF 0.995 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.73 · 1 PDB
- Residue 2001
- the ferm 2 domain
Similar variants
- MYO7A p.Thr2001Met Uncertain significance ★★ ⚠ same residue
- MYO7A p.Ala1288Pro Likely pathogenic ★★★ same condition
- MYO7A p.Arg1168Gln Pathogenic ★★★ ⚠ same condition
- MYO7A p.Arg1873Gln Pathogenic ★★★ ⚠ same condition
- MYO7A p.Arg395Cys Likely pathogenic ★★★ ⚠ same condition
- MYO7A p.Arg668Cys Pathogenic ★★★ same condition
- MYO7A p.Arg853His Likely pathogenic ★★★ same condition
- MYO7A p.Glu968Asp Likely pathogenic ★★★ ⚠ same condition
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-thr2001 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown