MID1 p.Phe535=
c.1605T>C · rs768522341 · VCV587781
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.735%, mid)
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 5.7 | GERP 1, phastCons 1 |
| Overall | ||
| CADD | 10.94 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.735%
Middle Eastern · 32/4,354 alleles
Filtering AF
0.535%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.467%
Overall
0.0188%
228/1,209,861 alleles · rare
exomes 214/1,098,001 · genomes 14/111,860 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.735% | 136 |
| South Asian | 0.165% | 604 |
| Remaining individualsnot grpmax-eligible | 0.0273% | 3,662 |
| European (non-Finnish) | 0.00961% | 10,408 |
| Admixed American | 0.00437% | 22,876 |
| East Asian | 0.00296% | 33,757 |
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.Phe535=
- Coding
- c.1605T>C
- MANE Select
- NM_000381
- dbSNP
- rs768522341
- Type
- single nucleotide variant
- Location
- chrX:10454920 (GRCh38)
- Structure
- AlphaFold pLDDT 86.51 · 5 PDB
- Residue 535
- the b30.2/spry domain
Similar variants
- MID1 p.Phe535Leu Uncertain significance ★ ⚠ same residue
- 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
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-phe535 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown