Is DMD p.Arg889Ter (c.2665C>T) pathogenic?

DMD p.Arg889Ter (c.2665C>T) is classified Pathogenic in DMD (ClinVar, Multiple submitters, 8 submitters; last evaluated 2024-11-26). Absent from gnomAD v4.1; Associated with Becker muscular dystrophy.

What condition is associated with DMD p.Arg889Ter (c.2665C>T)?

DMD p.Arg889Ter (c.2665C>T) is associated with Becker muscular dystrophy, cardiomyopathy, dilated cardiomyopathy 3B (ClinVar).

How common is DMD p.Arg889Ter (c.2665C>T) in the general population?

DMD p.Arg889Ter (c.2665C>T) is absent from gnomAD v4.1 (gnomAD).

How is Becker muscular dystrophy inherited?

Typically X-linked recessive (Orphanet). A genetic counselor can assess individual risk for a family.

DMD p.Arg889Ter

c.2665C>T · rs1060502639 · VCV409911

Pathogenic Multiple submitters

Classification

Pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 8 submitters

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

Becker muscular dystrophy

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	nonsense (stop-gain)	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 21 of 79
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1	GERP -0.42, phastCons 0.99
Overall
CADD	34.0	PHRED · no single calibrated threshold — expert panels disagree

Predicted loss-of-function is descriptive, not an applied PVS1 code.

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.Arg889Ter
Coding: c.2665C>T
MANE Select: NM_004006
dbSNP: rs1060502639
Type: single nucleotide variant
Location: chrX:32485057 (GRCh38)

Full DMD gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Becker muscular dystrophy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: cardiomyopathy dilated cardiomyopathy 3B Duchenne muscular dystrophy neuromuscular disease caused by qualitative or quantitative defects of dystrophin

For Becker muscular dystrophy (Orphanet):

Inheritance: X-linked recessive
Onset: Adolescent, Adult, Childhood, Elderly
Prevalence: 1-9 / 100 000 (Europe)

Similar variants

DMD p.Arg889= Likely benign ★★ same residue
DMD p.Arg889Gly Uncertain significance ★ ⚠ same residue
DMD p.Arg889Leu 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

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-arg889ter (accessed [today's date]).

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