EHMT1 p.Pro809=
c.2427G>A · rs370924392 · VCV735810
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0217%, amr)
Conditions
2
Inborn genetic diseases
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 -3.3 | GERP -3.2 |
| Overall | ||
| CADD | 2.772 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0217%
Admixed American · 13/60,010 alleles
Filtering AF
0.0127%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0101%
Overall
0.00242%
39/1,614,082 alleles · ultra-rare
exomes 34/1,461,894 · genomes 5/152,188 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0217% | 4,616 |
| East Asian | 0.00445% | 22,448 |
| South Asian | 0.00439% | 22,772 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,608 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,243 |
| European (non-Finnish) | 0.00136% | 73,753 |
| African / African-American | 0.00133% | 74,922 |
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
- EHMT1
- Protein
- p.Pro809=
- Coding
- c.2427G>A
- MANE Select
- NM_024757
- dbSNP
- rs370924392
- Type
- single nucleotide variant
- Location
- chr9:137790892 (GRCh38)
- Gene constraint
- LOEUF 0.159 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 64.89 · 22 PDB
- Residue 809
- an α-helix
Similar variants
- EHMT1 p.Pro809Leu Pathogenic/Likely pathogenic ★★ same residue
- EHMT1 p.Pro809Arg Likely pathogenic ★ same residue
- EHMT1 c.1370-1G>C Likely pathogenic ★★ same condition
- EHMT1 c.1647+2T>C Pathogenic/Likely pathogenic ★★ same condition
- EHMT1 c.2193-1G>C Pathogenic ★★ same condition
- EHMT1 c.2276-2A>G Pathogenic ★★ same condition
- EHMT1 c.2712+1G>A Pathogenic ★★ same condition
- EHMT1 c.2867+2T>C Pathogenic/Likely pathogenic ★★ 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/ehmt1-p-pro809 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown