MID1 p.Val546=
c.1638C>T · rs922580057 · VCV2718444
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00351%, sas)
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 6.6 | GERP 1.9, phastCons 1 |
| Overall | ||
| CADD | 9.264 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00351%
South Asian · 2/56,931 alleles
Filtering AF
0.000583%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000218%
Overall
0.000248%
3/1,210,303 alleles · very rare
exomes 3/1,096,812 · genomes 0/113,491 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00351% | 28,466 |
| Admixed American | 0.00217% | 46,037 |
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.Val546=
- Coding
- c.1638C>T
- MANE Select
- NM_000381
- dbSNP
- rs922580057
- Type
- single nucleotide variant
- Location
- chrX:10454887 (GRCh38)
- Structure
- AlphaFold pLDDT 86.51 · 5 PDB
- Residue 546
- the b30.2/spry domain; a β-strand
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-val546 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown