Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 8 submitters
gnomAD v4.1
Common
common (popmax 86.3%, eas) — too common for a highly-penetrant pathogenic allele
Conditions
1
macrocephaly-intellectual disability-neurodevelopmental disorder-small thorax syndrome
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 -0.28 | GERP -3.1, phastCons 0.001 |
| Overall | ||
| CADD | 1.893 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
86.3%
East Asian · 38,681/44,818 alleles
Filtering AF
85.6%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 85.3%
Overall
71.6%
1,154,239/1,612,826 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 86.3% | 1 |
| South Asian | 76.8% | 1 |
| Admixed American | 76.5% | 1 |
| Amishnot grpmax-eligible | 75.2% | 1 |
| Finnishnot grpmax-eligible | 74.8% | 1 |
| European (non-Finnish) | 73.1% | 1 |
| Middle Eastern | 72.7% | 1 |
| Remaining individualsnot grpmax-eligible | 71.2% | 1 |
| Ashkenazi Jewishnot grpmax-eligible | 65.7% | 2 |
| African / African-American | 28.2% | 4 |
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.Asp479=
- Coding
- c.1437T>C
- MANE Select
- NM_004958
- dbSNP
- rs1135172
- Type
- single nucleotide variant
- Location
- chr1:11241657 (GRCh38)
- Gene constraint
- LOEUF 0.268 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 78.57 · 73 PDB
- Residue 479
- an α-helix; the 'interaction with nbn' region
Similar variants
- MTOR p.Cys1483Tyr Pathogenic ★★★ same condition
- MTOR p.Thr1977Lys Pathogenic ★★★ same condition
- MTOR p.Trp1490Arg Likely pathogenic ★★★ same condition
- MTOR p.Glu1799Lys Pathogenic ★★ ⚠ same condition
- MTOR p.Glu2419Lys Pathogenic ★★ same condition
- MTOR p.Met2327Ile Pathogenic ★★ same condition
- MTOR p.Phe1888Cys Pathogenic/Likely pathogenic ★★ same condition
- MTOR p.Ser2413Ile 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/mtor-p-asp479 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown