Is DMD p.Arg2098Ter (c.6292C>T) pathogenic?

DMD p.Arg2098Ter (c.6292C>T) is classified Pathogenic in DMD (ClinVar, Multiple submitters, 7 submitters; last evaluated 2026-01-26). Very rare (popmax 0.000112%, nfe); Associated with X-linked DMD-related disorders.

What condition is associated with DMD p.Arg2098Ter (c.6292C>T)?

DMD p.Arg2098Ter (c.6292C>T) is associated with X-linked DMD-related disorders, Duchenne muscular dystrophy (ClinVar).

How common is DMD p.Arg2098Ter (c.6292C>T) in the general population?

DMD p.Arg2098Ter (c.6292C>T) is very rare (popmax 0.000112%, nfe) (gnomAD).

DMD p.Arg2098Ter

c.6292C>T · rs128626250 · VCV11260

Pathogenic Multiple submitters

Classification

Pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 7 submitters

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.000112%, nfe)

Conditions

X-linked DMD-related disorders

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 44 of 79
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.97	GERP -3.2, phastCons 0.082
Overall
CADD	35.0	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

Grpmax group 0.000112% European (non-Finnish) · 1/892,504 alleles

Overall 9.14e-05% 1/1,094,540 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.Arg2098Ter
Coding: c.6292C>T
MANE Select: NM_004006
dbSNP: rs128626250
Type: single nucleotide variant
Location: chrX:32217062 (GRCh38)

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

Disease context

X-linked DMD-related disorders

Also linked: Duchenne muscular dystrophy

Similar variants

DMD p.Arg2098Gln Likely benign ★★ same residue
DMD p.Arg2098= Likely benign ★ 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-arg2098ter (accessed [today's date]).

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