EMX2 p.Pro116=
c.348G>T · rs144775289 · VCV502001
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0299%, nfe)
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 1.2 | GERP 0.52, phastCons 1 |
| Overall | ||
| CADD | 12.09 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0299%
European (non-Finnish) · 353/1,179,604 alleles
Filtering AF
0.0273%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0263%
Overall
0.023%
371/1,612,754 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0299% | 3,342 |
| Middle Eastern | 0.0164% | 6,080 |
| Remaining individualsnot grpmax-eligible | 0.0128% | 7,806 |
| Admixed American | 0.00668% | 14,975 |
| African / African-American | 0.00536% | 18,661 |
| South Asian | 0.0011% | 91,054 |
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.Pro116=
- Coding
- c.348G>T
- MANE Select
- NM_004098
- dbSNP
- rs144775289
- Type
- single nucleotide variant
- Location
- chr10:117543615 (GRCh38)
- Gene constraint
- LOEUF 0.499 · pLI 0.98 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 67.26
Similar variants
- EMX2 p.Ser192Thr Uncertain significance ★★ ⚠ same type
- EMX2 c.591+6T>C Benign/Likely benign ★★ same type
- EMX2 p.Ala35= Benign/Likely benign ★★ same type
- EMX2 p.Arg156= Benign ★★ same type
- EMX2 p.Lys199Gln Likely pathogenic ★ same type
- EMX2 p.Val83Leu Pathogenic ★ ⚠ same type
- EMX2 p.Ala172Asp Uncertain significance ★ ⚠ same type
- EMX2 p.Ala172Thr 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/emx2-p-pro116 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown