MTOR p.Leu170=
c.510G>C · rs12120294 · VCV695385
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 7 submitters
gnomAD v4.1
Rare
rare (popmax 0.599%, nfe)
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 -0.35 | GERP -0.68, phastCons 0.052 |
| Overall | ||
| CADD | 7.039 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.599%
European (non-Finnish) · 7,070/1,179,784 alleles
Filtering AF
0.588%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.583%
Overall
0.491%
7,925/1,613,562 alleles · rare
exomes 7,397/1,461,256 · genomes 528/152,306 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.599% | 167 |
| Remaining individualsnot grpmax-eligible | 0.376% | 266 |
| Admixed American | 0.252% | 397 |
| South Asian | 0.235% | 425 |
| Finnishnot grpmax-eligible | 0.209% | 478 |
| African / African-American | 0.12% | 834 |
| Middle Eastern | 0.116% | 866 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0811% | 1,232 |
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.Leu170=
- Coding
- c.510G>C
- MANE Select
- NM_004958
- dbSNP
- rs12120294
- Type
- single nucleotide variant
- Location
- chr1:11256187 (GRCh38)
- Gene constraint
- LOEUF 0.268 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 78.57 · 73 PDB
- Residue 170
- 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-leu170 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown