MID1 p.Ser433=
c.1299G>A · rs143673869 · VCV92874
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.19%, afr)
Conditions
1
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 -20 | GERP -3.9 |
| Overall | ||
| CADD | 0.399 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.19%
African / African-American · 678/57,199 alleles
Filtering AF
1.11%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.08%
Overall
0.062%
749/1,207,743 alleles · low-frequency
exomes 363/1,095,821 · genomes 386/111,922 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.19% | 84 |
| Remaining individualsnot grpmax-eligible | 0.0714% | 1,400 |
| Middle Eastern | 0.046% | 2,176 |
| Admixed American | 0.0327% | 3,054 |
| South Asian | 0.0106% | 9,472 |
| European (non-Finnish) | 0.00156% | 63,913 |
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.Ser433=
- Coding
- c.1299G>A
- MANE Select
- NM_000381
- dbSNP
- rs143673869
- Type
- single nucleotide variant
- Location
- chrX:10459794 (GRCh38)
- Structure
- AlphaFold pLDDT 86.51 · 5 PDB
- Residue 433
- the fibronectin type-iii domain
Similar variants
- MID1 p.Ser433Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
- MID1 p.Ala211Pro Uncertain significance ★★ ⚠ same condition
- MID1 p.Arg291Thr Uncertain significance ★★ ⚠ same condition
- MID1 p.Arg472Cys Uncertain significance ★★ ⚠ same condition
- MID1 p.Asn234Lys Uncertain significance ★★ ⚠ same condition
- MID1 p.Asp180Asn Uncertain significance ★★ ⚠ same condition
- MID1 p.Gly529Ala Uncertain significance ★★ ⚠ same condition
- MID1 p.Ser225Asn 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-ser433 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown