DMD p.Arg13Lys
c.38G>A · rs587780918 · VCV137109
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
AlphaMissense
likely benign
0.2557 · ACMG-weighted
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| AlphaMissense | 0.2557 | likely benign |
|---|---|---|
| REVEL | 0.626 | indeterminate |
| SaProt | — | not scored · why |
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP 7.5 | GERP -0.73, phastCons 1 |
| Regional constraint | o/e 1.36 | unconstrained · MANE · 1,863 kb · p 2.4e-62 · regional, not allelic |
| Overall | ||
| CADD | 25.8 | PHRED · no single calibrated threshold — expert panels disagree |
AlphaMissense carries the ACMG weight for missense; REVEL is an independent agreement signal.
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.Arg13Lys
- Coding
- c.38G>A
- MANE Select
- NM_004006
- dbSNP
- rs587780918
- Type
- single nucleotide variant
- Location
- chrX:33020194 (GRCh38)
- Residue 13
- the 'actin-binding' region
Similar variants
- DMD p.Arg13Ser Uncertain significance ★ ⚠ same residue
- DMD c.10086+1G>A Pathogenic ★★ same type
- DMD c.10086+1G>T Pathogenic ★★ same type
- DMD c.10086+2T>C Pathogenic ★★ same type
- DMD c.10087-2A>G Pathogenic/Likely pathogenic ★★ same type
- DMD c.10223+1G>A Pathogenic ★★ same type
- DMD c.10223+1G>C Pathogenic ★★ same type
- DMD c.10224-2A>G Likely pathogenic ★★ same type
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-arg13lys (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown