MTOR p.Cys626=
c.1878C>T · rs79942701 · VCV414903
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.83%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.6 | GERP -3.1, phastCons 1 |
| Overall | ||
| CADD | 7.661 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.83%
African / African-American · 2,873/75,052 alleles
Filtering AF
3.71%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.66%
Overall
0.197%
3,183/1,614,206 alleles · low-frequency
exomes 1,584/1,461,892 · genomes 1,599/152,314 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.83% | 26 |
| Remaining individualsnot grpmax-eligible | 0.254% | 393 |
| Admixed American | 0.187% | 536 |
| Middle Eastern | 0.099% | 1,010 |
| South Asian | 0.0121% | 8,281 |
| European (non-Finnish) | 0.00186% | 53,638 |
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.Cys626=
- Coding
- c.1878C>T
- MANE Select
- NM_004958
- dbSNP
- rs79942701
- Type
- single nucleotide variant
- Location
- chr1:11238526 (GRCh38)
- Gene constraint
- LOEUF 0.268 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 78.57 · 73 PDB
- Residue 626
- an α-helix; the 'interaction with nbn' region
Similar variants
- 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
- MTOR p.Thr1977Arg 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-cys626 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown