MID1 p.Ser455=
c.1365C>T · rs752455741 · VCV2986229
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.196%, eas)
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 -5.6 | GERP -3.9 |
| Overall | ||
| CADD | 0.902 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.196%
East Asian · 66/33,752 alleles
Filtering AF
0.158%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.144%
Overall
0.00893%
108/1,208,830 alleles · rare
exomes 98/1,096,609 · genomes 10/112,221 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.196% | 511 |
| Middle Eastern | 0.0695% | 1,439 |
| African / African-American | 0.0192% | 5,208 |
| South Asian | 0.0158% | 6,312 |
| Admixed American | 0.00872% | 11,465 |
| Remaining individualsnot grpmax-eligible | 0.0042% | 23,787 |
| European (non-Finnish) | 0.00145% | 68,776 |
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.Ser455=
- Coding
- c.1365C>T
- MANE Select
- NM_000381
- dbSNP
- rs752455741
- Type
- single nucleotide variant
- Location
- chrX:10459728 (GRCh38)
- Structure
- AlphaFold pLDDT 86.51 · 5 PDB
- Residue 455
- the fibronectin type-iii domain
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-ser455 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown