Is DMD p.Arg1459= (c.4377A>G) pathogenic?

DMD p.Arg1459= (c.4377A>G) is classified Likely benign in DMD (ClinVar, Multiple submitters, 2 submitters; last evaluated 2023-11-30). Very rare (popmax 0.00402%, nfe); Associated with Duchenne muscular dystrophy.

What condition is associated with DMD p.Arg1459= (c.4377A>G)?

DMD p.Arg1459= (c.4377A>G) is associated with Duchenne muscular dystrophy (ClinVar).

How common is DMD p.Arg1459= (c.4377A>G) in the general population?

DMD p.Arg1459= (c.4377A>G) is very rare (popmax 0.00402%, nfe) (gnomAD).

How is Duchenne muscular dystrophy inherited?

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

DMD p.Arg1459=

c.4377A>G · rs2097986992 · VCV1452980

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00402%, nfe)

Conditions

Duchenne muscular dystrophy

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · T>A here scores Δ0.49 · evaluated, not missing
Constraint at this position
Conservation	phyloP 0.21	GERP -5.3, phastCons 0.99
Overall
CADD	8.083	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00402% European (non-Finnish) · 36/894,758 alleles

Filtering AF 0.00295% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00261%

Overall 0.00306% 37/1,209,108 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00402%	24,854
Remaining individualsnot grpmax-eligible	0.0021%	47,575

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.Arg1459=
Coding: c.4377A>G
MANE Select: NM_004006
dbSNP: rs2097986992
Type: single nucleotide variant
Location: chrX:32389642 (GRCh38)
Residue 1459: the 'interaction with synm' 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.Arg1459Ter Pathogenic ★★ same residue
DMD p.Arg1459Leu Uncertain significance ★★ same residue
DMD p.Arg1459Gln Conflicting classifications of pathogenicity ★ ⚠ same residue
DMD p.Arg1459Pro 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

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-arg1459 (accessed [today's date]).

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