MID1 p.Asp71=
c.213C>T · rs1272432970 · VCV2986133
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0233%, mid)
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 5.5 | GERP -0.33, phastCons 1 |
| Overall | ||
| CADD | 11.35 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0233%
Middle Eastern · 1/4,296 alleles
Filtering AF
0.000819%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000631%
Overall
0.00159%
19/1,193,403 alleles · ultra-rare
exomes 18/1,081,682 · genomes 1/111,721 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0233% | 4,296 |
| Finnishnot grpmax-eligible | 0.00653% | 15,322 |
| South Asian | 0.00372% | 26,879 |
| European (non-Finnish) | 0.00147% | 68,121 |
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.Asp71=
- Coding
- c.213C>T
- MANE Select
- NM_000381
- dbSNP
- rs1272432970
- Type
- single nucleotide variant
- Location
- chrX:10567335 (GRCh38)
- Structure
- AlphaFold pLDDT 86.51 · 5 PDB
Similar variants
- 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
- MID1 p.Ala316Glu 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-asp71 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown