MPC1 p.Ala4=
c.12G>A · rs567798756 · VCV2886487
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00233%, eas)
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 0.048 | GERP 0.99, phastCons 0.91 |
| Overall | ||
| CADD | 12.17 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00233%
East Asian · 1/42,850 alleles
Overall
0.000188%
3/1,594,342 alleles · very rare
exomes 2/1,442,036 · genomes 1/152,306 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00233% | 42,850 |
| Admixed American | 0.00171% | 58,636 |
| Remaining individualsnot grpmax-eligible | 0.00162% | 61,642 |
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.Ala4=
- Coding
- c.12G>A
- MANE Select
- NM_016098
- dbSNP
- rs567798756
- Type
- single nucleotide variant
- Location
- chr6:166382865 (GRCh38)
- Gene constraint
- LOEUF 0.919 · pLI 0.10 (gnomAD)
- Structure
- AlphaFold pLDDT 92.85 · 13 PDB
Similar variants
- 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.Ala10= Benign/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-ala4 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown