Is DMD p.His3299fs (c.9897_9898del) pathogenic?

DMD p.His3299fs (c.98979898del) is classified Pathogenic in DMD (ClinVar, Single submitter, 1 submitter; last evaluated 2022-07-11). No gnomAD frequency available for this variant; Associated with Duchenne muscular dystrophy.

What condition is associated with DMD p.His3299fs (c.9897_9898del)?

DMD p.His3299fs (c.9897_9898del) is associated with Duchenne muscular dystrophy (ClinVar).

How common is DMD p.His3299fs (c.9897_9898del) in the general population?

DMD p.His3299fs (c.9897_9898del) is no gnomAD frequency available for this variant (gnomAD).

How is Duchenne muscular dystrophy inherited?

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

DMD p.His3299fs

c.9897_9898del · rs2041303734 · VCV949105

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Duchenne muscular dystrophy

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 68 of 79
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 6	GERP 3.4, phastCons 1

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

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: DMD
Protein: p.His3299fs
Coding: c.9897_9898del
MANE Select: NM_004006
dbSNP: rs2041303734
Type: Microsatellite
Location: chrX:31182814 (GRCh38)
Residue 3299: an α-helix; the 'interaction with synm' 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.His3299Arg Conflicting classifications of pathogenicity ★ ⚠ same residue
DMD p.Arg2205fs Pathogenic/Likely pathogenic ★★ same condition
DMD p.Arg822fs Pathogenic/Likely pathogenic ★★ same condition
DMD p.Arg978fs Pathogenic/Likely pathogenic ★★ same condition
DMD p.Asn2991fs Pathogenic ★★ same condition
DMD p.Asn3068fs Pathogenic ★★ same condition
DMD p.Asn837fs Pathogenic ★★ same condition
DMD p.Gln2131fs 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-his3299fs (accessed [today's date]).

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