EHMT1 p.Pro300=
c.900T>C · rs1554858785 · VCV531876
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000254%, 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 | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.28 | GERP -3.3, phastCons 0.43 |
| Overall | ||
| CADD | 8.376 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000254%
European (non-Finnish) · 3/1,180,002 alleles
Filtering AF
6.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.9e-05%
Overall
0.000186%
3/1,613,872 alleles · very rare
exomes 2/1,461,788 · genomes 1/152,084 · 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.Pro300=
- Coding
- c.900T>C
- MANE Select
- NM_024757
- dbSNP
- rs1554858785
- Type
- single nucleotide variant
- Location
- chr9:137743447 (GRCh38)
- Gene constraint
- LOEUF 0.159 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 64.89 · 22 PDB
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-pro300 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown