DMD p.Leu464=
c.1390C>T · rs2057403088 · VCV2450356
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00353%, afr)
Conditions
1
Cardiovascular phenotype
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 4.4 | GERP -0.18, phastCons 1 |
| Overall | ||
| CADD | 7.681 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00353%
African / African-American · 2/56,682 alleles
Filtering AF
0.000585%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000219%
Overall
0.000332%
4/1,204,689 alleles · very rare
exomes 3/1,094,426 · genomes 1/110,263 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00353% | 28,341 |
| European (non-Finnish) | 0.000224% | 445,933 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- DMD
- Protein
- p.Leu464=
- Coding
- c.1390C>T
- MANE Select
- NM_004006
- dbSNP
- rs2057403088
- Type
- single nucleotide variant
- Location
- chrX:32614395 (GRCh38)
Similar variants
- DMD c.2804-2A>C Pathogenic/Likely pathogenic ★★ same condition
- DMD c.31+1G>C Pathogenic ★★ same condition
- DMD c.3432+2036A>G Pathogenic/Likely pathogenic ★★ same condition
- DMD c.3433-1G>A Pathogenic ★★ same condition
- DMD c.357+1G>T Pathogenic ★★ same condition
- DMD c.9974+1G>A Pathogenic/Likely pathogenic ★★ same condition
- DMD p.Arg3034Ter Pathogenic ★★ same condition
- DMD p.Gln1144= 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-leu464 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown