MPC1 p.His101=
c.303C>T · rs12205572 · VCV138241
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Common
common (popmax 9.27%, mid) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>C here scores Δ0.22 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1 | GERP -4.8 |
| Overall | ||
| CADD | 1.135 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
9.27%
Middle Eastern · 561/6,050 alleles
Filtering AF
8.64%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 8.48%
Overall
5.33%
85,831/1,611,590 alleles · common
exomes 79,762/1,459,370 · genomes 6,069/152,220 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 9.27% | 11 |
| South Asian | 8.71% | 11 |
| Amishnot grpmax-eligible | 6.25% | 16 |
| Finnishnot grpmax-eligible | 5.67% | 18 |
| European (non-Finnish) | 5.65% | 18 |
| Remaining individualsnot grpmax-eligible | 5.32% | 19 |
| Ashkenazi Jewishnot grpmax-eligible | 4.42% | 23 |
| Admixed American | 2.81% | 36 |
| African / African-American | 0.96% | 104 |
| East Asian | 0.0223% | 4,486 |
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.His101=
- Coding
- c.303C>T
- MANE Select
- NM_016098
- dbSNP
- rs12205572
- Type
- single nucleotide variant
- Location
- chr6:166365976 (GRCh38)
- Gene constraint
- LOEUF 0.919 · pLI 0.10 (gnomAD)
- Structure
- AlphaFold pLDDT 92.85 · 13 PDB
- Residue 101
- an α-helix
Similar variants
- MPC1 p.His101Tyr Likely benign ★ 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.Ala10= Benign/Likely 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-his101 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown