MGLL p.Pro146=
c.438G>A · rs111794060 · VCV767929
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.854%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.031 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -12 | GERP -4.3 |
| Overall | ||
| CADD | 0.111 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.854%
African / African-American · 641/75,048 alleles
Filtering AF
0.799%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.778%
Overall
0.0466%
752/1,614,198 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.854% | 117 |
| Remaining individualsnot grpmax-eligible | 0.107% | 933 |
| Admixed American | 0.035% | 2,858 |
| South Asian | 0.00878% | 11,386 |
| European (non-Finnish) | 0.00127% | 78,670 |
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
- MGLL
- Protein
- p.Pro146=
- Coding
- c.438G>A
- MANE Select
- NM_007283
- dbSNP
- rs111794060
- Type
- single nucleotide variant
- Location
- chr3:127721125 (GRCh38)
- Gene constraint
- LOEUF 0.5 · pLI 0.98 (gnomAD)
- Structure
- AlphaFold pLDDT 94.36 · 30 PDB
- Residue 146
- a β-strand
Similar variants
- MGLL p.Pro146Leu Uncertain significance ★ ⚠ same residue
- MGLL p.Ala136Thr Uncertain significance ★ ⚠ same type
- MGLL p.Ala174Val Uncertain significance ★ ⚠ same type
- MGLL p.Ala233Thr Uncertain significance ★ ⚠ same type
- MGLL p.Ala305Thr Uncertain significance ★ ⚠ same type
- MGLL p.Arg229Trp Uncertain significance ★ ⚠ same type
- MGLL p.Arg232His Uncertain significance ★ ⚠ same type
- MGLL p.Arg250Cys 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/mgll-p-pro146 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown