MGMT p.Pro87=
c.261C>T · rs144397748 · VCV721938
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0287%, 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 -1.7 | GERP -2.5 |
| Overall | ||
| CADD | 7.441 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0287%
European (non-Finnish) · 338/1,179,336 alleles
Filtering AF
0.0261%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0251%
Overall
0.0226%
364/1,612,434 alleles · ultra-rare
exomes 339/1,460,186 · genomes 25/152,248 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0287% | 3,489 |
| Admixed American | 0.0201% | 4,968 |
| Remaining individualsnot grpmax-eligible | 0.016% | 6,240 |
| African / African-American | 0.00267% | 37,447 |
| Finnishnot grpmax-eligible | 0.00156% | 63,900 |
| South Asian | 0.0011% | 91,008 |
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
- MGMT
- Protein
- p.Pro87=
- Coding
- c.261C>T
- MANE Select
- NM_002412
- dbSNP
- rs144397748
- Type
- single nucleotide variant
- Location
- chr10:129708030 (GRCh38)
- Gene constraint
- LOEUF 1.413 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.86 · 23 PDB
- Residue 87
- an α-helix
Similar variants
- MGMT p.Glu30Lys Likely benign ★★ same type
- MGMT p.Lys178Arg Benign ★★ same type
- MGMT c.-54C>G Uncertain significance ★ same type
- MGMT c.-60G>T Uncertain significance ★ same type
- MGMT p.Ala126Gly Uncertain significance ★ ⚠ same type
- MGMT p.Ala197Thr Uncertain significance ★ ⚠ same type
- MGMT p.Ala68Thr Uncertain significance ★ ⚠ same type
- MGMT p.Ala75Thr Uncertain significance ★ ⚠ 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/mgmt-p-pro87 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown