MID2 p.Thr194=
c.582C>A · rs766790109 · VCV794087
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0563%, 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 0.94 | GERP 1.9, phastCons 1 |
| Overall | ||
| CADD | 9.519 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0563%
East Asian · 19/33,744 alleles
Filtering AF
0.0368%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0306%
Overall
0.00232%
28/1,209,419 alleles · ultra-rare
exomes 23/1,097,970 · genomes 5/111,449 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0563% | 1,776 |
| Remaining individualsnot grpmax-eligible | 0.0189% | 5,289 |
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
- MID2
- Protein
- p.Thr194=
- Coding
- c.582C>A
- MANE Select
- NM_012216
- dbSNP
- rs766790109
- Type
- single nucleotide variant
- Location
- chrX:107841247 (GRCh38)
- Structure
- AlphaFold pLDDT 80.18 · 4 PDB
Similar variants
- MID2 p.Ala150Ser Uncertain significance ★★ ⚠ same type
- MID2 p.Arg121His Uncertain significance ★★ ⚠ same type
- MID2 p.Arg164Gly Uncertain significance ★★ ⚠ same type
- MID2 p.Ser60= Benign ★★ same type
- MID2 p.Arg105Pro Uncertain significance ★ ⚠ same type
- MID2 p.Arg121Cys Uncertain significance ★ ⚠ same type
- MID2 p.Arg121Leu Uncertain significance ★ ⚠ same type
- MID2 p.Arg122Gln Uncertain significance ★ ⚠ 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/mid2-p-thr194 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown