EMX2 p.Ala59del
c.161CCG[5] · rs756693906 · VCV1711265
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0253%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 3.1 | GERP -2.1, phastCons 1 |
| Overall | ||
| CADD | 21.7 | PHRED · no single calibrated threshold — expert panels disagree |
| Region caveats | ||
| Repeat context | tandem | (GCC)n simple repeat · ambiguous alignment · confidence, not pathogenicity |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0253%
European (non-Finnish) · 297/1,172,754 alleles
Filtering AF
0.023%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.022%
Overall
0.0205%
327/1,597,242 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0253% | 3,949 |
| Admixed American | 0.0171% | 5,835 |
| Remaining individualsnot grpmax-eligible | 0.00972% | 10,287 |
| African / African-American | 0.00805% | 12,415 |
| Finnishnot grpmax-eligible | 0.00494% | 20,245 |
| South Asian | 0.00448% | 22,311 |
| East Asian | 0.00228% | 43,770 |
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
- EMX2
- Protein
- p.Ala59del
- Coding
- c.161CCG[5]
- MANE Select
- NM_004098
- dbSNP
- rs756693906
- Type
- Microsatellite
- Location
- chr10:117543427 (GRCh38)
- Gene constraint
- LOEUF 0.499 · pLI 0.98 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 67.26
Similar variants
- EMX2 p.Ala59dup Conflicting classifications of pathogenicity ★ same residue
- EMX2 p.Ala58_Ala59dup Uncertain significance ★★ same type
- EMX2 p.Ala58_Ala59del Benign/Likely benign ★★ 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/emx2-p-ala59del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown