MID1 p.Asp129=
c.387C>T · rs777149623 · VCV1922099
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00437%, amr)
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 -0.3 | GERP -4.7, phastCons 0.004 |
| Overall | ||
| CADD | 1.607 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00437%
Admixed American · 2/45,735 alleles
Filtering AF
0.00161%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00137%
Overall
0.00223%
27/1,209,316 alleles · very rare
exomes 25/1,098,237 · genomes 2/111,079 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00437% | 22,867 |
| Remaining individualsnot grpmax-eligible | 0.0042% | 23,793 |
| East Asian | 0.00296% | 33,732 |
| European (non-Finnish) | 0.00246% | 40,685 |
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.Asp129=
- Coding
- c.387C>T
- MANE Select
- NM_000381
- dbSNP
- rs777149623
- Type
- single nucleotide variant
- Location
- chrX:10567161 (GRCh38)
- Structure
- AlphaFold pLDDT 86.51 · 5 PDB
Similar variants
- MID1 p.Asp129fs Likely pathogenic ★ same residue
- MID1 p.Ala130Thr Pathogenic/Likely pathogenic ★★ same type
- MID1 p.Arg277Ter Pathogenic ★★ same type
- MID1 p.Arg368Ter Pathogenic ★★ same type
- MID1 p.Arg495Ter Pathogenic ★★ same type
- MID1 c.864+4T>G Uncertain significance ★★ same type
- MID1 p.Ala114Thr Uncertain significance ★★ ⚠ same type
- MID1 p.Ala211Pro 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/mid1-p-asp129 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown