MID1 p.Ser410=
c.1230C>T · rs16986145 · VCV92873
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 8 submitters
gnomAD v4.1
Common
common (popmax 17.9%, afr) — too common for a highly-penetrant pathogenic allele
Conditions
1
Inborn genetic diseases
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 -1.7 | GERP -3.2 |
| Overall | ||
| CADD | 3.093 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
17.9%
African / African-American · 10,218/56,933 alleles
Filtering AF
17.7%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 17.5%
Overall
2.17%
26,223/1,208,032 alleles · common
exomes 19,665/1,096,432 · genomes 6,558/111,600 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 17.9% | 6 |
| Middle Eastern | 4.78% | 21 |
| South Asian | 3.32% | 30 |
| Remaining individualsnot grpmax-eligible | 2.69% | 37 |
| Admixed American | 1.69% | 59 |
| Ashkenazi Jewishnot grpmax-eligible | 1.38% | 72 |
| European (non-Finnish) | 1.25% | 80 |
| Finnishnot grpmax-eligible | 0.721% | 139 |
| East Asian | 0.139% | 718 |
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.Ser410=
- Coding
- c.1230C>T
- MANE Select
- NM_000381
- dbSNP
- rs16986145
- Type
- single nucleotide variant
- Location
- chrX:10469752 (GRCh38)
- Structure
- AlphaFold pLDDT 86.51 · 5 PDB
- Residue 410
- the fibronectin type-iii domain
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-ser410 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown