EGR2 p.Ala242=
c.726T>G · VCV4847175
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.004%, afr)
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 2.5 | GERP 1.6, phastCons 1 |
| Overall | ||
| CADD | 10.95 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.004%
African / African-American · 3/74,930 alleles
Filtering AF
0.00106%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000495%
Overall
0.000186%
3/1,614,084 alleles · very rare
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
- EGR2
- Protein
- p.Ala242=
- Coding
- c.726T>G
- MANE Select
- NM_000399
- Type
- single nucleotide variant
- Location
- chr10:62813912 (GRCh38)
- Gene constraint
- LOEUF 0.401 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 49.02
Similar variants
- EGR2 p.Arg359Trp Pathogenic ★★ same type
- EGR2 p.Arg381Cys Pathogenic ★★ same type
- EGR2 p.Arg381His Pathogenic ★★ same type
- EGR2 p.Arg381Leu Pathogenic ★★ same type
- EGR2 p.Arg409Gln Pathogenic/Likely pathogenic ★★ same type
- EGR2 p.Arg409Trp Pathogenic/Likely pathogenic ★★ same type
- EGR2 p.Glu356Gln Likely pathogenic ★★ ⚠ same type
- EGR2 p.Glu356Lys Pathogenic ★★ ⚠ 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/egr2-p-ala242 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown