Is DMD p.Arg563Cys (c.1687C>T) pathogenic?

DMD p.Arg563Cys (c.1687C>T) is classified Conflicting classifications of pathogenicity in DMD (ClinVar, Conflicting submitters, 8 submitters; last evaluated 2026-01-28). AlphaMissense: likely benign (0.0932); Ultra-rare (popmax 0.0105%, afr); Associated with Cardiovascular phenotype.

What condition is associated with DMD p.Arg563Cys (c.1687C>T)?

DMD p.Arg563Cys (c.1687C>T) is associated with Cardiovascular phenotype, Becker muscular dystrophy, dilated cardiomyopathy 3B (ClinVar).

How common is DMD p.Arg563Cys (c.1687C>T) in the general population?

DMD p.Arg563Cys (c.1687C>T) is ultra-rare (popmax 0.0105%, afr) (gnomAD).

What do computational predictors say about DMD p.Arg563Cys (c.1687C>T)?

AlphaMissense predicts likely benign (score 0.0932) — an in-silico prediction, not a clinical call.

DMD p.Arg563Cys

c.1687C>T · rs145739725 · VCV289591

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 8 submitters

AlphaMissense

likely benign

0.0932 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0105%, afr)

Missense predictors

0/2 damaging

AlphaMissense, REVEL

Conditions

Cardiovascular phenotype

Computational evidence

Protein change
AlphaMissense	0.0932	likely benign
REVEL	0.154	moderately benign-leaning
⇒ AlphaMissense and REVEL both call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.2	GERP -0.25, phastCons 0.97
Regional constraint	o/e 1.36	unconstrained · MANE · 1,863 kb · p 2.4e-62 · regional, not allelic
Overall
CADD	24.9	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 0.0105% African / African-American · 6/57,132 alleles

Filtering AF 0.00786% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00724%

Overall 0.0081% 98/1,209,239 alleles · ultra-rare

Ancestry group	Frequency	1 in
Remaining individualsnot grpmax-eligible	0.0105%	9,510
African / African-Americangrpmax	0.0105%	9,522
European (non-Finnish)	0.0095%	10,526
Ashkenazi Jewishnot grpmax-eligible	0.00454%	22,023
Admixed American	0.00219%	45,663

Remaining individuals shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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.Arg563Cys
Coding: c.1687C>T
MANE Select: NM_004006
dbSNP: rs145739725
Type: single nucleotide variant
Location: chrX:32573762 (GRCh38)

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: Becker muscular dystrophy dilated cardiomyopathy 3B Duchenne muscular dystrophy

Similar variants

DMD p.Arg563= Likely benign ★★ same residue
DMD p.Arg563His Conflicting classifications of pathogenicity ★ ⚠ same residue
DMD p.Arg563Ser Conflicting classifications of pathogenicity ★ ⚠ same residue
DMD p.Arg563fs Pathogenic ★ 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-arg563cys (accessed [today's date]).

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