Is DMD p.Glu501= (c.1503A>G) pathogenic?

DMD p.Glu501= (c.1503A>G) is classified Benign/Likely benign in DMD (ClinVar, Multiple submitters, 8 submitters; last evaluated 2026-01-10). Ultra-rare (popmax 0.0503%, amr); Associated with Cardiovascular phenotype.

What condition is associated with DMD p.Glu501= (c.1503A>G)?

DMD p.Glu501= (c.1503A>G) is associated with Cardiovascular phenotype, cardiomyopathy, Becker muscular dystrophy (ClinVar).

How common is DMD p.Glu501= (c.1503A>G) in the general population?

DMD p.Glu501= (c.1503A>G) is ultra-rare (popmax 0.0503%, amr) (gnomAD).

DMD p.Glu501=

c.1503A>G · rs770464589 · VCV227306

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 8 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0503%, amr)

Conditions

Cardiovascular phenotype

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.053	GERP -3.5, phastCons 0.96
Overall
CADD	3.388	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0503% Admixed American · 23/45,681 alleles

Filtering AF 0.0344% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0291%

Overall 0.0051% 61/1,195,391 alleles · ultra-rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0503%	1,986
Middle Eastern	0.0231%	4,325
Remaining individualsnot grpmax-eligible	0.00848%	11,789
European (non-Finnish)	0.00374%	26,725

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.Glu501=
Coding: c.1503A>G
MANE Select: NM_004006
dbSNP: rs770464589
Type: single nucleotide variant
Location: chrX:32595856 (GRCh38)
Residue 501: a UniProt-annotated variant site (in bmd)

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: cardiomyopathy Becker muscular dystrophy Duchenne muscular dystrophy

Similar variants

DMD p.Glu501Ter Pathogenic/Likely pathogenic ★★ same residue
DMD p.Glu501Gly 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

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-glu501 (accessed [today's date]).

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