Is EHMT1 p.Arg12Ser (c.36G>C) pathogenic?

EHMT1 p.Arg12Ser (c.36G>C) is classified Uncertain significance in EHMT1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-08-10). AlphaMissense: likely benign (0.2269); Very rare (popmax 0.00691%, amr); Associated with Kleefstra syndrome 1.

What condition is associated with EHMT1 p.Arg12Ser (c.36G>C)?

EHMT1 p.Arg12Ser (c.36G>C) is associated with Kleefstra syndrome 1 (ClinVar).

How common is EHMT1 p.Arg12Ser (c.36G>C) in the general population?

EHMT1 p.Arg12Ser (c.36G>C) is very rare (popmax 0.00691%, amr) (gnomAD).

What do computational predictors say about EHMT1 p.Arg12Ser (c.36G>C)?

AlphaMissense predicts likely benign (score 0.2269) — an in-silico prediction, not a clinical call.

EHMT1 p.Arg12Ser

c.36G>C · rs1025787561 · VCV1933097

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2269 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00691%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Kleefstra syndrome 1

Computational evidence

Protein change
AlphaMissense	0.2269	likely benign
REVEL	0.139	moderately benign-leaning
SaProt	LLR -5.22	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.1	GERP 0.11, phastCons 1
Regional constraint	o/e 1.20	unconstrained · MANE · 144 kb · p 1.3e-07 · regional, not allelic
Overall
CADD	19.89	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00691% Admixed American · 4/57,926 alleles

Filtering AF 0.00231% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00138%

Overall 0.000688% 11/1,598,648 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00691%	14,482
African / African-American	0.00134%	74,686
South Asian	0.00114%	87,864
European (non-Finnish)	0.000426%	234,676

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.Arg12Ser
Coding: c.36G>C
MANE Select: NM_024757
dbSNP: rs1025787561
Type: single nucleotide variant
Location: chr9:137710981 (GRCh38)
Gene constraint: LOEUF 0.159 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 64.89 · 22 PDB
Residue 12: the 'disordered' region

Full EHMT1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Kleefstra syndrome 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

EHMT1 p.Arg12Lys Benign/Likely benign ★★ same residue
EHMT1 p.Arg12Thr Conflicting classifications of pathogenicity ★ ⚠ same residue
EHMT1 p.Arg12= Likely benign ★ same residue
EHMT1 p.Arg12Met Benign ★ same residue
EHMT1 p.Arg12fs Pathogenic ★ 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

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-arg12ser (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown