MID1 p.Val139=
c.417A>G · rs1335960901 · VCV1738470
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00887%, eas)
Conditions
1
Inborn genetic diseases
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 0.81 | GERP -2.8, phastCons 1 |
| Overall | ||
| CADD | 9.348 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00887%
East Asian · 3/33,834 alleles
Filtering AF
0.00235%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00125%
Overall
0.000413%
5/1,211,461 alleles · very rare
exomes 5/1,098,161 · genomes 0/113,300 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00887% | 11,278 |
| Admixed American | 0.00434% | 23,018 |
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.Val139=
- Coding
- c.417A>G
- MANE Select
- NM_000381
- dbSNP
- rs1335960901
- Type
- single nucleotide variant
- Location
- chrX:10567131 (GRCh38)
- Structure
- AlphaFold pLDDT 86.51 · 5 PDB
- Residue 139
- a β-strand
Similar variants
- 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
- MID1 p.Thr393Ile 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-val139 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown