Is DMD p.Asp523Val (c.1568A>T) pathogenic?

DMD p.Asp523Val (c.1568A>T) is classified Likely benign in DMD (ClinVar, Single submitter, 1 submitter; last evaluated 2025-06-11). AlphaMissense: likely benign (0.3105); Very rare (popmax 0.00219%, amr); Associated with Duchenne muscular dystrophy.

What condition is associated with DMD p.Asp523Val (c.1568A>T)?

DMD p.Asp523Val (c.1568A>T) is associated with Duchenne muscular dystrophy (ClinVar).

How common is DMD p.Asp523Val (c.1568A>T) in the general population?

DMD p.Asp523Val (c.1568A>T) is very rare (popmax 0.00219%, amr) (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.Asp523Val (c.1568A>T)?

AlphaMissense predicts likely benign (score 0.3105) — an in-silico prediction, not a clinical call.

DMD p.Asp523Val

c.1568A>T · rs751216373 · VCV2154598

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.3105 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00219%, amr)

Conditions

Duchenne muscular dystrophy

Computational evidence

Protein change
AlphaMissense	0.3105	likely benign
REVEL	0.301	indeterminate
SaProt	—	not scored · why
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 7.8	GERP 1.7, phastCons 1
Regional constraint	o/e 1.36	unconstrained · MANE · 1,863 kb · p 2.4e-62 · regional, not allelic
Overall
CADD	24.0	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL is an independent agreement signal.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00219% Admixed American · 1/45,760 alleles

Overall 0.000165% 2/1,208,746 alleles · very rare exomes 1/1,096,575 · genomes 1/112,171 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00219%	45,760
African / African-American	0.00175%	57,237

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.Asp523Val
Coding: c.1568A>T
MANE Select: NM_004006
dbSNP: rs751216373
Type: single nucleotide variant
Location: chrX:32595791 (GRCh38)
Residue 523: a UniProt-annotated variant site (in bmd)

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.Asp523His 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-asp523val (accessed [today's date]).

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