Is DMD p.Arg3113Gln (c.9338G>A) pathogenic?

DMD p.Arg3113Gln (c.9338G>A) is classified Conflicting classifications of pathogenicity in DMD (ClinVar, Conflicting submitters, 7 submitters; last evaluated 2025-12-29). AlphaMissense: likely pathogenic (0.9813); Very rare (popmax 0.000112%, nfe); Associated with dilated cardiomyopathy 3B.

What condition is associated with DMD p.Arg3113Gln (c.9338G>A)?

DMD p.Arg3113Gln (c.9338G>A) is associated with dilated cardiomyopathy 3B, cardiomyopathy, Becker muscular dystrophy (ClinVar).

How common is DMD p.Arg3113Gln (c.9338G>A) in the general population?

DMD p.Arg3113Gln (c.9338G>A) is very rare (popmax 0.000112%, nfe) (gnomAD).

What do computational predictors say about DMD p.Arg3113Gln (c.9338G>A)?

AlphaMissense predicts likely pathogenic (score 0.9813) — an in-silico prediction, not a clinical call.

DMD p.Arg3113Gln

c.9338G>A · rs1556320083 · VCV455945

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 7 submitters

AlphaMissense

likely pathogenic

0.9813 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.000112%, nfe)

Conditions

dilated cardiomyopathy 3B

Computational evidence

Protein change
AlphaMissense	0.9813	likely pathogenic · top 5% in DMD
REVEL	0.584	indeterminate
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.7	GERP 3.4, phastCons 1
Regional constraint	o/e 0.66	unconstrained · MANE · 170 kb · p 2.6e-08 · regional, not allelic
Overall
CADD	29.8	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000112% European (non-Finnish) · 1/894,907 alleles

Overall 9.11e-05% 1/1,097,491 alleles · very rare

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.Arg3113Gln
Coding: c.9338G>A
MANE Select: NM_004006
dbSNP: rs1556320083
Type: single nucleotide variant
Location: chrX:31223070 (GRCh38)
Residue 3113: an α-helix; the 'interaction with synm' region

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

Disease context

dilated cardiomyopathy 3B — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: cardiomyopathy Becker muscular dystrophy Duchenne muscular dystrophy

Similar variants

DMD p.Arg3113Ter Pathogenic ★★ same residue
DMD p.Arg3113Gly Uncertain significance ★ ⚠ same residue
DMD p.Arg3113_Leu3115del Likely pathogenic ★ same residue
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

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-arg3113gln (accessed [today's date]).

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