Is EHMT1 p.Ser183fs (c.546dup) pathogenic?

EHMT1 p.Ser183fs (c.546dup) is classified Likely pathogenic in EHMT1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-07-05). Absent from gnomAD.

How common is EHMT1 p.Ser183fs (c.546dup) in the general population?

EHMT1 p.Ser183fs (c.546dup) is absent from gnomAD (gnomAD).

EHMT1 p.Ser183fs

c.546dup · rs2135511329 · VCV1695521

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a LoF-intolerant gene
NMD	predicted	premature termination codon in exon 3 of 27
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 6.5	GERP -0.44, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. 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.Ser183fs
Coding: c.546dup
MANE Select: NM_024757
dbSNP: rs2135511329
Type: Duplication
Location: chr9:137717082 (GRCh38)
Gene constraint: LOEUF 0.159 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 64.89 · 22 PDB
Residue 183: the 'disordered' region

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

Similar variants

EHMT1 p.Ser183Thr Uncertain significance ★ ⚠ same residue
EHMT1 p.Phe253fs Pathogenic/Likely pathogenic ★★ same type
EHMT1 p.Glu531_Ala536dup Uncertain significance ★★ same type
EHMT1 p.Ala193fs Pathogenic ★ same type
EHMT1 p.Arg1230fs Likely pathogenic ★ same type
EHMT1 p.Arg291fs Likely pathogenic ★ same type
EHMT1 p.Asn1106fs Pathogenic ★ same type
EHMT1 p.Asn240fs Pathogenic ★ 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/ehmt1-p-ser183fs (accessed [today's date]).

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