MGP p.Ala11=
c.33C>T · rs142282008 · VCV734625
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.005%, amr)
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 -0.29 | GERP -3.7, phastCons 0.001 |
| Overall | ||
| CADD | 5.855 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.005%
Admixed American · 3/59,988 alleles
Filtering AF
0.00145%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00123%
Overall
0.00192%
31/1,613,684 alleles · very rare
exomes 26/1,461,474 · genomes 5/152,210 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.005% | 19,996 |
| African / African-American | 0.00267% | 37,463 |
| East Asian | 0.00223% | 44,882 |
| European (non-Finnish) | 0.00212% | 47,191 |
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
- MGP
- Protein
- p.Ala11=
- Coding
- c.33C>T
- MANE Select
- NM_000900
- dbSNP
- rs142282008
- Type
- single nucleotide variant
- Location
- chr12:14885759 (GRCh38)
- Gene constraint
- LOEUF 1.63 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 82.56 · 3 PDB
Similar variants
- MGP c.94+1G>A Pathogenic/Likely pathogenic ★★ same type
- MGP c.94+5G>A Uncertain significance ★★ same type
- MGP p.Arg61His Uncertain significance ★★ ⚠ same type
- MGP p.Gln47Glu Uncertain significance ★★ ⚠ same type
- MGP p.Met26Thr Uncertain significance ★★ ⚠ same type
- MGP p.Tyr76His Uncertain significance ★★ ⚠ same type
- MGP c.171-67T>A Likely benign ★★ same type
- MGP c.61+10T>G Likely benign ★★ 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/mgp-p-ala11 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown