Is EMD p.Asp93del (c.274GAC[1]) pathogenic?

EMD p.Asp93del (c.274GAC[1]) is classified Uncertain significance in EMD (ClinVar, Single submitter, 1 submitter; last evaluated 2024-09-22). Very rare (popmax 9.12e-05%); Associated with Emery-Dreifuss muscular dystrophy 1, X-linked.

What condition is associated with EMD p.Asp93del (c.274GAC[1])?

EMD p.Asp93del (c.274GAC[1]) is associated with Emery-Dreifuss muscular dystrophy 1, X-linked (ClinVar).

How common is EMD p.Asp93del (c.274GAC[1]) in the general population?

EMD p.Asp93del (c.274GAC[1]) is very rare (popmax 9.12e-05%) (gnomAD).

EMD p.Asp93del

c.274GAC[1] · VCV3362547

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 9.12e-05%)

Conditions

Emery-Dreifuss muscular dystrophy 1, X-linked

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -2.1	GERP -0.68

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 9.12e-05%

Overall 9.12e-05% 1/1,096,389 alleles · very rare

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: EMD
Protein: p.Asp93del
Coding: c.274GAC[1]
MANE Select: NM_000117
Type: Microsatellite
Location: chrX:154380242 (GRCh38)
Structure: AlphaFold pLDDT 61.26 · 6 PDB
Residue 93: the 'interaction with f-actin' region

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

Disease context

Emery-Dreifuss muscular dystrophy 1, X-linked — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

EMD p.Asp93Tyr Uncertain significance ★★ ⚠ same residue
EMD p.Lys37del Conflicting classifications of pathogenicity ★ same condition
EMD c.265+1G>A Likely pathogenic ★★ same condition
EMD c.450-2A>G Pathogenic/Likely pathogenic ★★ same condition
EMD p.Asn20fs Pathogenic/Likely pathogenic ★★ same condition
EMD p.Gln44Ter Pathogenic ★★ same condition
EMD p.Leu225fs Pathogenic/Likely pathogenic ★★ same condition
EMD p.Leu84fs 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/emd-p-asp93del (accessed [today's date]).

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