EHMT2 p.Cys987=
c.2961C>T · rs148424397 · VCV2656431
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.154%, nfe)
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 -3.8 | GERP -4.2 |
| Overall | ||
| CADD | 3.61 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.154%
European (non-Finnish) · 1,816/1,179,942 alleles
Filtering AF
0.148%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.146%
Overall
0.124%
1,999/1,612,886 alleles · rare
exomes 1,808/1,460,580 · genomes 191/152,306 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.154% | 650 |
| Admixed American | 0.15% | 667 |
| Remaining individualsnot grpmax-eligible | 0.0784% | 1,275 |
| Finnishnot grpmax-eligible | 0.0556% | 1,798 |
| Middle Eastern | 0.0165% | 6,060 |
| African / African-American | 0.008% | 12,505 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,600 |
| South Asian | 0.0011% | 91,038 |
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
- EHMT2
- Protein
- p.Cys987=
- Coding
- c.2961C>T
- MANE Select
- NM_006709
- dbSNP
- rs148424397
- Type
- single nucleotide variant
- Location
- chr6:31883395 (GRCh38)
- Gene constraint
- LOEUF 0.492 · pLI 0.86 (gnomAD)
- Structure
- AlphaFold pLDDT 69.25 · 34 PDB
- Residue 987
- an α-helix; a binding site; the pre-set domain
Similar variants
- EHMT2 p.Ala1077Thr Pathogenic ★★ same type
- EHMT2 p.Ala1077Ser Pathogenic ★ same type
- EHMT2 p.Asn1112Ser Pathogenic ★ ⚠ same type
- EHMT2 p.Lys1162Arg Pathogenic ★ same type
- EHMT2 p.Phe1158Leu Pathogenic ★ same type
- EHMT2 c.328+2T>G Uncertain significance ★ same type
- EHMT2 p.Ala137Ser Uncertain significance ★ ⚠ same type
- EHMT2 p.Ala17Pro Uncertain significance ★ ⚠ same type
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/ehmt2-p-cys987 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown