DMD p.Arg3286Ter
c.9856A>T · rs2520024317 · VCV1725520
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
progressive muscular dystrophy
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 in a haploinsufficient gene (ClinGen) |
|---|---|---|
| NMD | predicted | premature termination codon in exon 68 of 79 |
| REVEL | 0.135 | moderately benign-leaning |
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.6 | GERP -4.8, phastCons 1 |
| Overall | ||
| CADD | 36.0 | 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
- DMD
- Protein
- p.Arg3286Ter
- Coding
- c.9856A>T
- MANE Select
- NM_004006
- dbSNP
- rs2520024317
- Type
- single nucleotide variant
- Location
- chrX:31182856 (GRCh38)
- Residue 3286
- an α-helix; the 'interaction with synm' region
Similar variants
- DMD p.Arg3286= Uncertain significance same residue
- DMD c.2168+2T>C Pathogenic/Likely pathogenic ★★ same condition
- DMD c.960+1G>A Likely pathogenic ★★ same condition
- DMD p.Arg768Ter Pathogenic ★★ same condition
- DMD p.Gln1054Ter Pathogenic/Likely pathogenic ★★ same condition
- DMD p.Gln1932Ter Pathogenic/Likely pathogenic ★★ same condition
- DMD p.Glu1795Ter Pathogenic/Likely pathogenic ★★ same condition
- DMD p.Glu3032Ter Pathogenic/Likely 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/dmd-p-arg3286ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown