EMD p.Ser60fs
c.178del · VCV3366307
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
Emery-Dreifuss muscular dystrophy 1, X-linked
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 2 of 6 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 0.2 | GERP -2.4, phastCons 0.007 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- EMD
- Protein
- p.Ser60fs
- Coding
- c.178del
- MANE Select
- NM_000117
- Type
- Deletion
- Location
- chrX:154379785 (GRCh38)
- Structure
- AlphaFold pLDDT 61.26 · 6 PDB
- Residue 60
- a modified residue (phosphoserine); the 'interaction with f-actin' region
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.Ser52fs Pathogenic ★★ same condition
- EMD p.Ser143_Glu144delinsTer Pathogenic ★ same condition
- EMD p.Ser60Arg Uncertain significance ★ ⚠ same residue
- EMD p.Ser60= Likely benign ★ same residue
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-ser60fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown