Is DMD p.Ala699Gly (c.2096C>G) pathogenic?

DMD p.Ala699Gly (c.2096C>G) is classified Conflicting classifications of pathogenicity in DMD (ClinVar, Conflicting submitters, 10 submitters; last evaluated 2026-02-01). AlphaMissense: likely benign (0.097); Rare (popmax 0.498%, eas); Associated with Cardiovascular phenotype.

What condition is associated with DMD p.Ala699Gly (c.2096C>G)?

DMD p.Ala699Gly (c.2096C>G) is associated with Cardiovascular phenotype, cardiomyopathy, Becker muscular dystrophy (ClinVar).

How common is DMD p.Ala699Gly (c.2096C>G) in the general population?

DMD p.Ala699Gly (c.2096C>G) is rare (popmax 0.498%, eas) (gnomAD).

What do computational predictors say about DMD p.Ala699Gly (c.2096C>G)?

AlphaMissense predicts likely benign (score 0.097) — an in-silico prediction, not a clinical call.

DMD p.Ala699Gly

c.2096C>G · rs202008454 · VCV194741

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 10 submitters

AlphaMissense

likely benign

0.097 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.498%, eas)

Missense predictors

0/2 damaging

AlphaMissense, REVEL

Conditions

Cardiovascular phenotype

Computational evidence

Protein change
AlphaMissense	0.097	likely benign
REVEL	0.127	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 4.4	GERP 0.15, phastCons 1
Regional constraint	o/e 1.36	unconstrained · MANE · 1,863 kb · p 2.4e-62 · regional, not allelic
Overall
CADD	20.9	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 0.498% East Asian · 168/33,733 alleles

Filtering AF 0.437% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.413%

Overall 0.0168% 203/1,208,596 alleles · rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.498%	201
South Asian	0.0387%	2,581
Remaining individualsnot grpmax-eligible	0.0252%	3,965
European (non-Finnish)	0.000112%	894,039

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.Ala699Gly
Coding: c.2096C>G
MANE Select: NM_004006
dbSNP: rs202008454
Type: single nucleotide variant
Location: chrX:32545231 (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: cardiomyopathy Becker muscular dystrophy dilated cardiomyopathy 3B Duchenne muscular dystrophy

Similar variants

DMD p.Ala699= Likely benign ★ same residue
DMD p.Ala699Thr 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-ala699gly (accessed [today's date]).

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