MTOR p.Glu804=
c.2412A>G · rs573881829 · VCV695851
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.83%, sas)
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 -0.072 | GERP 0.33, phastCons 0.001 |
| Overall | ||
| CADD | 7.681 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.83%
South Asian · 3,490/91,066 alleles
Filtering AF
3.73%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.68%
Overall
0.227%
3,670/1,614,064 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 3.83% | 26 |
| Remaining individualsnot grpmax-eligible | 0.226% | 443 |
| Middle Eastern | 0.115% | 866 |
| East Asian | 0.00891% | 11,218 |
| African / African-American | 0.00666% | 15,010 |
| Admixed American | 0.005% | 20,007 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,600 |
| European (non-Finnish) | 0.00161% | 62,103 |
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.Glu804=
- Coding
- c.2412A>G
- MANE Select
- NM_004958
- dbSNP
- rs573881829
- Type
- single nucleotide variant
- Location
- chr1:11233407 (GRCh38)
- Gene constraint
- LOEUF 0.268 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 78.57 · 73 PDB
- Residue 804
- an α-helix
Similar variants
- MTOR p.Glu804Gly Uncertain significance ★ ⚠ same residue
- MTOR p.Glu804Lys Uncertain significance ★ ⚠ 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
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-glu804 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown