Is DMD p.Arg3630Gln (c.10889G>A) pathogenic?

DMD p.Arg3630Gln (c.10889G>A) is classified Conflicting classifications of pathogenicity in DMD (ClinVar, Conflicting submitters, 6 submitters; last evaluated 2025-12-09). AlphaMissense: likely benign (0.1314); Very rare (popmax 0.000894%, nfe); Associated with Cardiovascular phenotype.

What condition is associated with DMD p.Arg3630Gln (c.10889G>A)?

DMD p.Arg3630Gln (c.10889G>A) is associated with Cardiovascular phenotype, Duchenne muscular dystrophy (ClinVar).

How common is DMD p.Arg3630Gln (c.10889G>A) in the general population?

DMD p.Arg3630Gln (c.10889G>A) is very rare (popmax 0.000894%, nfe) (gnomAD).

What do computational predictors say about DMD p.Arg3630Gln (c.10889G>A)?

AlphaMissense predicts likely benign (score 0.1314) — an in-silico prediction, not a clinical call.

DMD p.Arg3630Gln

c.10889G>A · rs1057522606 · VCV386803

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 6 submitters

AlphaMissense

likely benign

0.1314 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.000894%, nfe)

Missense predictors

0/2 damaging

AlphaMissense, REVEL

Conditions

Cardiovascular phenotype

Computational evidence

Protein change
AlphaMissense	0.1314	likely benign
REVEL	0.205	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 5.9	GERP 3.3, phastCons 1
Regional constraint	o/e 1.13	unconstrained · MANE · 25 kb · p 0.27 · regional, not allelic
Overall
CADD	26.2	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 0.000894% European (non-Finnish) · 8/894,733 alleles

Filtering AF 0.000385% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000278%

Overall 0.000662% 8/1,209,282 alleles · very rare

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.Arg3630Gln
Coding: c.10889G>A
MANE Select: NM_004006
dbSNP: rs1057522606
Type: single nucleotide variant
Location: chrX:31146323 (GRCh38)
Residue 3630: the 'disordered' region

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: Duchenne muscular dystrophy

Similar variants

DMD p.Arg3630Ter Likely 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
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-arg3630gln (accessed [today's date]).

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