Is DMD p.Cys3476= (c.10428C>T) pathogenic?

DMD p.Cys3476= (c.10428C>T) is classified Likely benign in DMD (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-08-21). Very rare (popmax 0.00662%, amr); Associated with Cardiovascular phenotype.

What condition is associated with DMD p.Cys3476= (c.10428C>T)?

DMD p.Cys3476= (c.10428C>T) is associated with Cardiovascular phenotype, Duchenne muscular dystrophy (ClinVar).

How common is DMD p.Cys3476= (c.10428C>T) in the general population?

DMD p.Cys3476= (c.10428C>T) is very rare (popmax 0.00662%, amr) (gnomAD).

DMD p.Cys3476=

c.10428C>T · rs190867451 · VCV1086701

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00662%, amr)

Conditions

Cardiovascular phenotype

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.189	benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 9.9	GERP 2.4, phastCons 1
Overall
CADD	11.79	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00662% Admixed American · 3/45,325 alleles

Filtering AF 0.00176% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000887%

Overall 0.000581% 7/1,204,770 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00662%	15,108
Remaining individualsnot grpmax-eligible	0.00633%	15,789
European (non-Finnish)	0.000112%	892,204

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.Cys3476=
Coding: c.10428C>T
MANE Select: NM_004006
dbSNP: rs190867451
Type: single nucleotide variant
Location: chrX:31169568 (GRCh38)
Residue 3476: the 'binds to sntb1' region

Full DMD gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Cardiovascular phenotype — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: Duchenne muscular dystrophy

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-cys3476 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown