EHMT1 p.Pro10=
c.30G>A · rs369073742 · VCV764164
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.033%, mid)
Conditions
1
Kleefstra syndrome 1
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 -0.38 | GERP -0.94, phastCons 0.011 |
| Overall | ||
| CADD | 8.973 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.033%
Middle Eastern · 2/6,060 alleles
Filtering AF
0.00582%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00304%
Overall
0.00163%
26/1,597,204 alleles · ultra-rare
exomes 21/1,445,070 · genomes 5/152,134 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.033% | 3,030 |
| Admixed American | 0.0104% | 9,617 |
| Remaining individualsnot grpmax-eligible | 0.00323% | 30,916 |
| East Asian | 0.00226% | 44,218 |
| European (non-Finnish) | 0.00119% | 83,765 |
| South Asian | 0.00114% | 87,734 |
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.Pro10=
- Coding
- c.30G>A
- MANE Select
- NM_024757
- dbSNP
- rs369073742
- Type
- single nucleotide variant
- Location
- chr9:137710975 (GRCh38)
- Gene constraint
- LOEUF 0.159 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 64.89 · 22 PDB
- Residue 10
- the 'disordered' region
Similar variants
- EHMT1 p.Pro10Leu Uncertain significance ★ ⚠ 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
- EHMT1 c.3036-1G>A 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-pro10 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown