Is EMD c.265+12del pathogenic?

EMD c.265+12del is classified Benign in EMD (ClinVar, Single submitter, 1 submitter; last evaluated 2025-04-28). Associated with X-linked Emery-Dreifuss muscular dystrophy.

What condition is associated with EMD c.265+12del?

EMD c.265+12del is associated with X-linked Emery-Dreifuss muscular dystrophy (ClinVar).

How is Emery-Dreifuss muscular dystrophy inherited?

Typically Autosomal dominant, Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

EMD c.265+12del

VCV4697494

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

Conditions

X-linked Emery-Dreifuss muscular dystrophy

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
Splice region	donor +12	near-intronic (+12 nt from the splice site)
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.063	GERP -2
Non-coding constraint	—	not assessed · autosomes only, so chrX has no window · absence ≠ unconstrained

Variant & gene context

Gene: EMD
Coding: c.265+12del
MANE Select: NM_000117
Type: Deletion
Location: chrX:154380028 (GRCh38)
Structure: AlphaFold pLDDT 61.26 · 6 PDB

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

Disease context

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

For Emery-Dreifuss muscular dystrophy (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive, X-linked recessive
Onset: Childhood
Prevalence: 1-9 / 1 000 000 (Europe)

Similar variants

EMD p.Asn20fs Pathogenic/Likely pathogenic ★★ same condition
EMD p.Leu225fs Pathogenic/Likely pathogenic ★★ same condition
EMD p.Leu84fs Pathogenic ★★ same condition
EMD p.Phe39fs Pathogenic ★★ same condition
EMD p.Pro208fs Pathogenic ★★ same condition
EMD p.Ser52fs Pathogenic ★★ same condition
EMD p.Tyr41fs Pathogenic ★★ same condition
EMD p.Phe39del 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/emd-c-265-plus-12del (accessed [today's date]).

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