Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.18%, mid)
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 1.1 | GERP -0.82, phastCons 1 |
| Overall | ||
| CADD | 13.72 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.18%
Middle Eastern · 132/6,062 alleles
Filtering AF
1.91%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.9%
Overall
1.69%
27,257/1,614,126 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 2.18% | 46 |
| Finnishnot grpmax-eligible | 1.93% | 52 |
| European (non-Finnish) | 1.93% | 52 |
| Remaining individualsnot grpmax-eligible | 1.52% | 66 |
| South Asian | 1.14% | 87 |
| Ashkenazi Jewishnot grpmax-eligible | 1.07% | 93 |
| Admixed American | 1.03% | 97 |
| African / African-American | 0.269% | 372 |
| East Asian | 0.0156% | 6,411 |
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.Arg156=
- Coding
- c.466C>A
- MANE Select
- NM_004098
- dbSNP
- rs8192642
- Type
- single nucleotide variant
- Location
- chr10:117545691 (GRCh38)
- Gene constraint
- LOEUF 0.499 · pLI 0.98 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 67.26
- Residue 156
- a DNA-binding region
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.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
- EMX2 p.Ala34Val 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-arg156 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown