EHMT2 p.His404=
c.1212C>T · rs369022743 · VCV758863
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0606%, 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 1.2 | GERP -1.3, phastCons 1 |
| Overall | ||
| CADD | 7.332 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0606%
Middle Eastern · 3/4,950 alleles
Filtering AF
0.0164%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00877%
Overall
0.00119%
19/1,598,080 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0606% | 1,650 |
| African / African-American | 0.00268% | 37,308 |
| Admixed American | 0.00176% | 56,754 |
| Remaining individualsnot grpmax-eligible | 0.00162% | 61,832 |
| European (non-Finnish) | 0.00102% | 97,861 |
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.His404=
- Coding
- c.1212C>T
- MANE Select
- NM_006709
- dbSNP
- rs369022743
- Type
- single nucleotide variant
- Location
- chr6:31888973 (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-his404 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown