MID1 p.Leu79=
c.237A>G · rs773584650 · VCV2183163
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0198%, nfe)
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 0.46 | GERP -2.9, phastCons 1 |
| Overall | ||
| CADD | 8.672 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0198%
European (non-Finnish) · 175/885,074 alleles
Filtering AF
0.0173%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0165%
Overall
0.0161%
192/1,192,592 alleles · ultra-rare
exomes 181/1,081,152 · genomes 11/111,440 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0198% | 5,058 |
| Remaining individualsnot grpmax-eligible | 0.0192% | 5,205 |
| Finnishnot grpmax-eligible | 0.0109% | 9,193 |
| South Asian | 0.00373% | 26,842 |
| African / African-American | 0.00176% | 56,731 |
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.Leu79=
- Coding
- c.237A>G
- MANE Select
- NM_000381
- dbSNP
- rs773584650
- Type
- single nucleotide variant
- Location
- chrX:10567311 (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-leu79 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown