DMD p.Val3400=
c.10200C>G · rs1373944162 · VCV742494
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00175%, afr)
Conditions
2
Cardiovascular phenotype
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.074 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP 2.7 | GERP 1.7, phastCons 1 |
| Overall | ||
| CADD | 6.146 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00175%
African / African-American · 1/57,247 alleles
Overall
8.27e-05%
1/1,209,339 alleles · very rare
exomes 0/1,097,107 · genomes 1/112,232 · joint denominator
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.Val3400=
- Coding
- c.10200C>G
- MANE Select
- NM_004006
- dbSNP
- rs1373944162
- Type
- single nucleotide variant
- Location
- chrX:31178692 (GRCh38)
- Residue 3400
- the 'interaction with synm' region
Similar variants
- DMD c.10086+1G>A Pathogenic ★★ same condition
- DMD c.10086+1G>T Pathogenic ★★ same condition
- DMD c.10086+2T>C Pathogenic ★★ same condition
- DMD c.10087-2A>G Pathogenic/Likely pathogenic ★★ same condition
- DMD c.10223+1G>A Pathogenic ★★ same condition
- DMD c.10223+1G>C Pathogenic ★★ same condition
- DMD c.10224-2A>G Likely pathogenic ★★ same condition
- DMD c.10554-2A>G 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-val3400 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown