Is DMD p.Arg3489Cys (c.10465C>T) pathogenic?

DMD p.Arg3489Cys (c.10465C>T) is classified Conflicting classifications of pathogenicity in DMD (ClinVar, Conflicting submitters, 2 submitters; last evaluated 2025-02-06). AlphaMissense: likely benign (0.2419); Very rare (popmax 0.00296%, eas); Associated with Duchenne muscular dystrophy.

What condition is associated with DMD p.Arg3489Cys (c.10465C>T)?

DMD p.Arg3489Cys (c.10465C>T) is associated with Duchenne muscular dystrophy (ClinVar).

How common is DMD p.Arg3489Cys (c.10465C>T) in the general population?

DMD p.Arg3489Cys (c.10465C>T) is very rare (popmax 0.00296%, eas) (gnomAD).

How is Duchenne muscular dystrophy inherited?

Typically X-linked recessive (Orphanet). A genetic counselor can assess individual risk for a family.

What do computational predictors say about DMD p.Arg3489Cys (c.10465C>T)?

AlphaMissense predicts likely benign (score 0.2419) — an in-silico prediction, not a clinical call.

DMD p.Arg3489Cys

c.10465C>T · rs771240938 · VCV290290

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.2419 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00296%, eas)

Conditions

Duchenne muscular dystrophy

Computational evidence

Protein change
AlphaMissense	0.2419	likely benign
REVEL	0.549	indeterminate
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 5.2	GERP 3.4, phastCons 1
Regional constraint	o/e 0.57	unconstrained · MANE · 25 kb · p 7.9e-06 · regional, not allelic
Overall
CADD	29.2	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 0.00296% East Asian · 1/33,741 alleles

Overall 9.17e-05% 1/1,090,336 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.Arg3489Cys
Coding: c.10465C>T
MANE Select: NM_004006
dbSNP: rs771240938
Type: single nucleotide variant
Location: chrX:31169531 (GRCh38)
Residue 3489: the 'binds to sntb1' region

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

Disease context

Duchenne muscular dystrophy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Duchenne muscular dystrophy (Orphanet):

Inheritance: X-linked recessive
Onset: Childhood
Prevalence: 1-9 / 100 000 (Worldwide)

Similar variants

DMD p.Arg3489His Uncertain significance ★ 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
DMD c.10223+1G>C Pathogenic ★★ same condition
DMD c.10224-2A>G 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-arg3489cys (accessed [today's date]).

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