MTOR p.Ala607=
c.1821G>A · rs55881943 · VCV414906
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
rare (popmax 0.243%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.65 | acceptor gain · deltas |
|---|---|---|
| Pangolin | Δ0.34 | gain · loss 0.07 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP -3.7 | GERP -1.7 |
| Overall | ||
| CADD | 21.7 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.243%
East Asian · 109/44,862 alleles
Filtering AF
0.206%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.192%
Overall
0.0219%
353/1,613,488 alleles · rare
exomes 324/1,461,208 · genomes 29/152,280 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.243% | 412 |
| Remaining individualsnot grpmax-eligible | 0.032% | 3,124 |
| South Asian | 0.0253% | 3,959 |
| European (non-Finnish) | 0.0162% | 6,175 |
| African / African-American | 0.0107% | 9,379 |
| Admixed American | 0.00333% | 29,992 |
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
- MTOR
- Protein
- p.Ala607=
- Coding
- c.1821G>A
- MANE Select
- NM_004958
- dbSNP
- rs55881943
- Type
- single nucleotide variant
- Location
- chr1:11238583 (GRCh38)
- Gene constraint
- LOEUF 0.268 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 78.57 · 73 PDB
- Residue 607
- an α-helix; the 'interaction with nbn' region
Similar variants
- MTOR p.Ala607Val Likely benign ★ ⚠ same residue
- MTOR p.Ala1669Ser Likely pathogenic ★★★ ⚠ same type
- MTOR p.Cys1483Arg Pathogenic ★★★ same type
- MTOR p.Cys1483Tyr Pathogenic ★★★ same type
- MTOR p.Leu1460Pro Pathogenic ★★★ same type
- MTOR p.Leu2427Pro Pathogenic ★★★ same type
- MTOR p.Ser2215Phe Pathogenic ★★★ same type
- MTOR p.Ser2215Tyr 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/mtor-p-ala607 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown