EMD p.Cys147Ter
c.441C>A · rs2522789929 · VCV2627908
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
nonsense (stop-gain)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 | nonsense (stop-gain) | predicted loss-of-function |
|---|---|---|
| NMD | escapes | premature termination codon within the last 50 nt of the penultimate exon (5 of 6, 8 nt from its 3' end) — the truncated protein is likely expressed. PVS1 input, not an applied code |
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>T here scores Δ0.62 · evaluated, not missing |
| Constraint at this position | ||
| Conservation | phyloP 4.3 | GERP 0.35, phastCons 1 |
| Overall | ||
| CADD | 34.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- EMD
- Protein
- p.Cys147Ter
- Coding
- c.441C>A
- MANE Select
- NM_000117
- dbSNP
- rs2522789929
- Type
- single nucleotide variant
- Location
- chrX:154380794 (GRCh38)
- Structure
- AlphaFold pLDDT 61.26 · 6 PDB
- Residue 147
- the 'interaction with f-actin' region
Similar variants
- EMD p.Cys147= Uncertain significance ★ same residue
- EMD c.265+1G>A Likely pathogenic ★★ same condition
- EMD c.450-2A>G Pathogenic/Likely pathogenic ★★ same condition
- EMD p.Gln44Ter Pathogenic ★★ same condition
- EMD c.82+3A>G Uncertain significance ★★ same condition
- EMD p.Ala55Ser Uncertain significance ★★ ⚠ same condition
- EMD p.Arg152His Uncertain significance ★★ ⚠ same condition
- EMD p.Arg204Cys 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-p-cys147ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown