Is DMD p.Arg488= (c.1464C>T) pathogenic?

DMD p.Arg488= (c.1464C>T) is classified Likely benign in DMD (ClinVar, Single submitter, 3 submitters; last evaluated 2026-01-14). Ultra-rare (popmax 0.0179%, eas); Associated with Duchenne muscular dystrophy.

What condition is associated with DMD p.Arg488= (c.1464C>T)?

DMD p.Arg488= (c.1464C>T) is associated with Duchenne muscular dystrophy, cardiomyopathy, Becker muscular dystrophy (ClinVar).

How common is DMD p.Arg488= (c.1464C>T) in the general population?

DMD p.Arg488= (c.1464C>T) is ultra-rare (popmax 0.0179%, eas) (gnomAD).

How is Duchenne muscular dystrophy inherited?

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

DMD p.Arg488=

c.1464C>T · rs771891715 · VCV1114758

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0179%, eas)

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 · G>C here scores Δ0.21 · evaluated, not missing
Constraint at this position
Conservation	phyloP 2.1	GERP -0.19, phastCons 1
Overall
CADD	7.568	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0179% East Asian · 6/33,591 alleles

Filtering AF 0.00769% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00529%

Overall 0.000663% 8/1,205,779 alleles · ultra-rare exomes 6/1,096,178 · genomes 2/109,601 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0179%	5,599
Admixed American	0.00221%	45,329
Remaining individualsnot grpmax-eligible	0.00211%	47,447

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.Arg488=
Coding: c.1464C>T
MANE Select: NM_004006
dbSNP: rs771891715
Type: single nucleotide variant
Location: chrX:32614321 (GRCh38)

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

Also linked: cardiomyopathy Becker muscular dystrophy

For Duchenne muscular dystrophy (Orphanet):

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

Similar variants

DMD p.Arg488Cys Benign/Likely benign ★★ same residue
DMD p.Arg488His Conflicting classifications of pathogenicity ★ ⚠ same residue
DMD p.Arg488Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
DMD p.Arg488Ser 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-arg488 (accessed [today's date]).

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