MTOR p.Asp2485=
c.7455C>T · rs41274506 · VCV695429
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 10 submitters
gnomAD v4.1
Rare
rare (popmax 0.527%, nfe)
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 -4 | GERP -3.8 |
| Overall | ||
| CADD | 1.06 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.527%
European (non-Finnish) · 6,221/1,179,834 alleles
Filtering AF
0.516%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.512%
Overall
0.436%
7,029/1,613,964 alleles · rare
exomes 6,529/1,461,614 · genomes 500/152,350 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.527% | 190 |
| Middle Eastern | 0.313% | 319 |
| Remaining individualsnot grpmax-eligible | 0.294% | 340 |
| South Asian | 0.248% | 403 |
| African / African-American | 0.211% | 475 |
| Admixed American | 0.178% | 561 |
| Ashkenazi Jewishnot grpmax-eligible | 0.159% | 630 |
| Finnishnot grpmax-eligible | 0.105% | 956 |
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.Asp2485=
- Coding
- c.7455C>T
- MANE Select
- NM_004958
- dbSNP
- rs41274506
- Type
- single nucleotide variant
- Location
- chr1:11109363 (GRCh38)
- Gene constraint
- LOEUF 0.268 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 78.57 · 73 PDB
Similar variants
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- 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-asp2485 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown