EHMT1 p.Arg445=
c.1335G>A · rs1564697340 · VCV589381
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000169%, nfe)
Conditions
1
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 0.32, phastCons 1 |
| Overall | ||
| CADD | 10.52 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000169%
European (non-Finnish) · 2/1,180,008 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000124%
2/1,614,142 alleles · very rare
exomes 2/1,461,848 · genomes 0/152,294 · joint denominator
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.Arg445=
- Coding
- c.1335G>A
- MANE Select
- NM_024757
- dbSNP
- rs1564697340
- Type
- single nucleotide variant
- Location
- chr9:137754257 (GRCh38)
- Gene constraint
- LOEUF 0.159 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 64.89 · 22 PDB
- Residue 445
- the 'disordered' region
Similar variants
- EHMT1 c.2193-1G>C Pathogenic ★★ same condition
- EHMT1 p.Arg1116Ter Pathogenic ★★ same condition
- EHMT1 p.Arg291Ter Pathogenic ★★ same condition
- EHMT1 p.Arg490Ter Pathogenic/Likely pathogenic ★★ same condition
- EHMT1 p.Trp437Ter Pathogenic/Likely pathogenic ★★ same condition
- EHMT1 c.3461+3G>A Uncertain significance ★★ same condition
- EHMT1 c.-5G>A Uncertain significance ★★ same condition
- EHMT1 p.Ala1295Val Uncertain significance ★★ ⚠ 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-arg445 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown