Is EMX2 p.Glu215= (c.645G>A) pathogenic?

EMX2 p.Glu215= (c.645G>A) is classified Likely benign in EMX2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-05-13). Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with EMX2 p.Glu215= (c.645G>A)?

EMX2 p.Glu215= (c.645G>A) is associated with Inborn genetic diseases (ClinVar).

How common is EMX2 p.Glu215= (c.645G>A) in the general population?

EMX2 p.Glu215= (c.645G>A) is absent from gnomAD v4.1 (gnomAD).

EMX2 p.Glu215=

c.645G>A · VCV4017912

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.219	benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 5	GERP 1.7, phastCons 1
Overall
CADD	10.91	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: EMX2
Protein: p.Glu215=
Coding: c.645G>A
MANE Select: NM_004098
Type: single nucleotide variant
Location: chr10:117548118 (GRCh38)
Gene constraint: LOEUF 0.499 · pLI 0.98 · ClinGen HI 1/3 (gnomAD)
Structure: AlphaFold pLDDT 67.26
Residue 215: the 'disordered' region

Full EMX2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

EMX2 p.Ala172Asp Uncertain significance ★ ⚠ same condition
EMX2 p.Ala172Thr Uncertain significance ★ ⚠ same condition
EMX2 p.Ala34Val Uncertain significance ★ ⚠ same condition
EMX2 p.Ala5Gly Uncertain significance ★ ⚠ same condition
EMX2 p.Ala5Pro Uncertain significance ★ ⚠ same condition
EMX2 p.Ala95Val Uncertain significance ★ ⚠ same condition
EMX2 p.Arg114Gly Uncertain significance ★ ⚠ same condition
EMX2 p.Asn80Asp 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/emx2-p-glu215 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown