MPC1 p.Ala10=
c.30G>A · rs79498685 · VCV378152
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.28%, afr)
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 -1.5 | GERP -3.1 |
| Overall | ||
| CADD | 9.47 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.28%
African / African-American · 934/72,970 alleles
Filtering AF
1.21%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.18%
Overall
0.0727%
1,161/1,596,498 alleles · low-frequency
exomes 561/1,444,208 · genomes 600/152,290 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.28% | 78 |
| Admixed American | 0.101% | 994 |
| Remaining individualsnot grpmax-eligible | 0.0923% | 1,084 |
| Middle Eastern | 0.0498% | 2,007 |
| European (non-Finnish) | 0.00912% | 10,966 |
| South Asian | 0.00113% | 88,654 |
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
- MPC1
- Protein
- p.Ala10=
- Coding
- c.30G>A
- MANE Select
- NM_016098
- dbSNP
- rs79498685
- Type
- single nucleotide variant
- Location
- chr6:166382847 (GRCh38)
- Gene constraint
- LOEUF 0.919 · pLI 0.10 (gnomAD)
- Structure
- AlphaFold pLDDT 92.85 · 13 PDB
- Residue 10
- an α-helix
Similar variants
- MPC1 p.Ala10Gly Uncertain significance ★ ⚠ same residue
- MPC1 p.Arg76Gln Uncertain significance ★★ ⚠ same type
- MPC1 p.Glu102Lys Uncertain significance ★★ ⚠ same type
- MPC1 p.Thr106Met Uncertain significance ★★ ⚠ same type
- MPC1 c.72-8C>T Likely benign ★★ same type
- MPC1 p.His101= Benign ★★ same type
- MPC1 p.Leu36Ile Benign ★★ same type
- MPC1 p.Ala70Thr Likely 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/mpc1-p-ala10 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown