Is DMD p.Asp219Val (c.656A>T) pathogenic?

DMD p.Asp219Val (c.656A>T) is classified Uncertain significance in DMD (ClinVar, Single submitter, 1 submitter; last evaluated 2021-08-31). AlphaMissense: likely benign (0.153); Absent from gnomAD v4.1; Associated with Duchenne muscular dystrophy.

What condition is associated with DMD p.Asp219Val (c.656A>T)?

DMD p.Asp219Val (c.656A>T) is associated with Duchenne muscular dystrophy (ClinVar).

How common is DMD p.Asp219Val (c.656A>T) in the general population?

DMD p.Asp219Val (c.656A>T) is absent from gnomAD v4.1 (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.Asp219Val (c.656A>T)?

AlphaMissense predicts likely benign (score 0.153) — an in-silico prediction, not a clinical call.

DMD p.Asp219Val

c.656A>T · rs2147607407 · VCV1512743

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.153 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

Duchenne muscular dystrophy

Computational evidence

Protein change
AlphaMissense	0.153	likely benign
REVEL	0.364	indeterminate
SaProt	—	not scored · why
Splicing
SpliceAI	Δ0.43	acceptor gain · deltas
Pangolin	Δ0.41	gain · loss 0.09 · agrees with SpliceAI · independent
Constraint at this position
Conservation	phyloP 9.9	GERP 5.2, phastCons 1
Regional constraint	o/e 1.36	unconstrained · MANE · 1,863 kb · p 2.4e-62 · regional, not allelic
Overall
CADD	27.2	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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: DMD
Protein: p.Asp219Val
Coding: c.656A>T
MANE Select: NM_004006
dbSNP: rs2147607407
Type: single nucleotide variant
Location: chrX:32699287 (GRCh38)
Residue 219: a β-strand; the calponin-homology (ch) 2 domain; the 'actin-binding' region

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.Asp219Glu Conflicting classifications of pathogenicity ★ same residue
DMD p.Asp219= Likely benign ★ same residue
DMD p.Asp219fs Pathogenic ★ same residue
DMD p.Asp219His 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

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-asp219val (accessed [today's date]).

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