EHMT1 p.Lys390=
c.1170G>A · rs1442452133 · VCV1007040
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00339%, nfe)
Conditions
1
Kleefstra syndrome 1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>T here scores Δ0.20 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 12 | GERP 1.5, phastCons 1 |
| Overall | ||
| CADD | 22.3 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00339%
European (non-Finnish) · 40/1,180,048 alleles
Filtering AF
0.00255%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00225%
Overall
0.00248%
40/1,613,898 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
- EHMT1
- Protein
- p.Lys390=
- Coding
- c.1170G>A
- MANE Select
- NM_024757
- dbSNP
- rs1442452133
- Type
- single nucleotide variant
- Location
- chr9:137744090 (GRCh38)
- Gene constraint
- LOEUF 0.159 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 64.89 · 22 PDB
- Residue 390
- the 'disordered' region
Similar variants
- 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
- EHMT1 c.3259-1G>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-lys390 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown