Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 8 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.88%, amr)
Conditions
2
Inborn genetic diseases
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 -1.8 | GERP -4.7 |
| Overall | ||
| CADD | 6.548 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.88%
Admixed American · 2,231/45,742 alleles
Filtering AF
4.71%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.64%
Overall
0.224%
2,712/1,209,747 alleles · low-frequency
exomes 2,290/1,098,240 · genomes 422/111,507 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 4.88% | 21 |
| East Asian | 0.4% | 250 |
| Remaining individualsnot grpmax-eligible | 0.263% | 381 |
| African / African-American | 0.0842% | 1,188 |
| South Asian | 0.0264% | 3,785 |
| European (non-Finnish) | 0.0176% | 5,666 |
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
- MID1
- Protein
- p.Pro166=
- Coding
- c.498G>A
- MANE Select
- NM_000381
- dbSNP
- rs7391874
- Type
- single nucleotide variant
- Location
- chrX:10567050 (GRCh38)
- Structure
- AlphaFold pLDDT 86.51 · 5 PDB
Similar variants
- MID1 p.Pro166Leu Uncertain significance ★ ⚠ same residue
- MID1 p.Ala130Thr Pathogenic/Likely pathogenic ★★ same condition
- MID1 p.Arg277Ter Pathogenic ★★ same condition
- MID1 p.Arg368Ter Pathogenic ★★ same condition
- MID1 p.Arg495Ter Pathogenic ★★ same condition
- MID1 p.Ala114Thr Uncertain significance ★★ ⚠ same condition
- MID1 p.Ala211Pro Uncertain significance ★★ ⚠ same condition
- MID1 p.Arg291Thr Uncertain significance ★★ ⚠ same condition
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/mid1-p-pro166 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown