EMID1 p.Pro69Leu
c.206C>T · rs147118853 · VCV3088579
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.118%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.236 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 4.7 | GERP 0.65, phastCons 1 |
| Regional constraint | o/e 0.98 | unconstrained · MANE · 53 kb · p 0.62 · regional, not allelic |
| Overall | ||
| CADD | 31.0 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.118%
Middle Eastern · 7/5,924 alleles
Filtering AF
0.0704%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0641%
Overall
0.00787%
121/1,537,444 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.118% | 846 |
| African / African-American | 0.0876% | 1,141 |
| South Asian | 0.0207% | 4,837 |
| Admixed American | 0.0139% | 7,181 |
| Finnishnot grpmax-eligible | 0.0101% | 9,933 |
| Remaining individualsnot grpmax-eligible | 0.00505% | 19,791 |
| European (non-Finnish) | 0.0015% | 66,887 |
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
- EMID1
- Protein
- p.Pro69Leu
- Coding
- c.206C>T
- MANE Select
- NM_133455
- dbSNP
- rs147118853
- Type
- single nucleotide variant
- Location
- chr22:29215030 (GRCh38)
- Gene constraint
- LOEUF 0.994 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 51.77
- Residue 69
- a disulfide bond; the emi domain
Similar variants
- EMID1 c.587-5C>G Benign ★★ same type
- EMID1 p.Ala108Thr Uncertain significance ★ same type
- EMID1 p.Ala112Thr Uncertain significance ★ same type
- EMID1 p.Ala127Ser Uncertain significance ★ same type
- EMID1 p.Ala28Thr Uncertain significance ★ same type
- EMID1 p.Ala409Val Uncertain significance ★ same type
- EMID1 p.Ala435Asp Uncertain significance ★ same type
- EMID1 p.Ala6Ser 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/emid1-p-pro69leu (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown