Is EHMT1 p.Ala928Ser (c.2782G>T) pathogenic?

EHMT1 p.Ala928Ser (c.2782G>T) is classified Uncertain significance in EHMT1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-11-05). AlphaMissense: likely benign (0.1187); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with EHMT1 p.Ala928Ser (c.2782G>T)?

EHMT1 p.Ala928Ser (c.2782G>T) is associated with Inborn genetic diseases (ClinVar).

How common is EHMT1 p.Ala928Ser (c.2782G>T) in the general population?

EHMT1 p.Ala928Ser (c.2782G>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about EHMT1 p.Ala928Ser (c.2782G>T)?

AlphaMissense predicts likely benign (score 0.1187) — an in-silico prediction, not a clinical call.

EHMT1 p.Ala928Ser

c.2782G>T · VCV4618302

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1187 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,610,858)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1187	likely benign
REVEL	0.06	moderately benign-leaning
SaProt	LLR -7.50	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 12	GERP 1.9, phastCons 1
Regional constraint	o/e 0.57	unconstrained · MANE · 35 kb · p 1.6e-15 · regional, not allelic
Overall
CADD	24.9	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

No allele count reported in gnomAD v4.1 (AN 1,610,858). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: EHMT1
Protein: p.Ala928Ser
Coding: c.2782G>T
MANE Select: NM_024757
Type: single nucleotide variant
Location: chr9:137811530 (GRCh38)
Gene constraint: LOEUF 0.159 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 64.89 · 22 PDB

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

EHMT1 p.Ala928Thr Uncertain significance ★★ ⚠ same residue
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

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-ala928ser (accessed [today's date]).

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