EHMT2 p.Thr264=
c.792G>A · rs151312506 · VCV716121
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 2%, 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 -11 | GERP -4.8 |
| Overall | ||
| CADD | 3.968 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2%
African / African-American · 1,499/75,014 alleles
Filtering AF
1.91%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.88%
Overall
0.121%
1,950/1,613,000 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2% | 50 |
| Admixed American | 0.287% | 349 |
| Remaining individualsnot grpmax-eligible | 0.189% | 530 |
| Middle Eastern | 0.099% | 1,010 |
| European (non-Finnish) | 0.0125% | 7,973 |
| South Asian | 0.00769% | 13,011 |
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
- EHMT2
- Protein
- p.Thr264=
- Coding
- c.792G>A
- MANE Select
- NM_006709
- dbSNP
- rs151312506
- Type
- single nucleotide variant
- Location
- chr6:31892479 (GRCh38)
- Gene constraint
- LOEUF 0.492 · pLI 0.86 (gnomAD)
- Structure
- AlphaFold pLDDT 69.25 · 34 PDB
Similar variants
- EHMT2 p.Ala1077Thr Pathogenic ★★ same type
- EHMT2 p.Ala1077Ser Pathogenic ★ same type
- EHMT2 p.Asn1112Ser Pathogenic ★ ⚠ same type
- EHMT2 p.Lys1162Arg Pathogenic ★ same type
- EHMT2 p.Phe1158Leu Pathogenic ★ same type
- EHMT2 c.328+2T>G Uncertain significance ★ same type
- EHMT2 p.Ala137Ser Uncertain significance ★ ⚠ same type
- EHMT2 p.Ala17Pro 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/ehmt2-p-thr264 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown