Is DMD p.Ser1513fs (c.4538_4541del) pathogenic?

DMD p.Ser1513fs (c.45384541del) is classified Pathogenic in DMD (ClinVar, Multiple submitters, 4 submitters; last evaluated 2025-10-07). No gnomAD frequency available for this variant; Associated with Becker muscular dystrophy, Cardiomyopathy, Duchenne muscular dystrophy, Dystrophin deficiency.

How common is DMD p.Ser1513fs (c.4538_4541del) in the general population?

DMD p.Ser1513fs (c.4538_4541del) is no gnomAD frequency available for this variant (gnomAD).

DMD p.Ser1513fs

Q: What condition is associated with DMD p.Ser1513fs (c.4538_4541del)?

DMD p.Ser1513fs (c.4538_4541del) is associated with Becker muscular dystrophy, Cardiomyopathy, Duchenne muscular dystrophy, Dystrophin deficiency, Duchenne muscular dystrophy (ClinVar).

c.4538_4541del · rs1064793479 · VCV418861

Pathogenic Multiple submitters

Classification

Pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Becker muscular dystrophy, Cardiomyopathy, Duchenne muscular dystrophy, Dystrophin deficiency

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 33 of 79
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 1.1	GERP -1.4, 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.Ser1513fs
Coding: c.4538_4541del
MANE Select: NM_004006
dbSNP: rs1064793479
Type: Deletion
Location: chrX:32386443 (GRCh38)
Residue 1513: the 'interaction with synm' region

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

Disease context

Becker muscular dystrophy, Cardiomyopathy, Duchenne muscular dystrophy, Dystrophin deficiency

Also linked: Duchenne muscular dystrophy

Similar variants

DMD p.Ser1513Arg Uncertain significance ★ same residue
DMD p.Ser1513= Likely benign ★ same residue
DMD c.1813-29_1813-2del Likely pathogenic ★★ same condition
DMD c.2804-1del Pathogenic ★★ same condition
DMD c.3433-5_3434del Pathogenic ★★ same condition
DMD c.4519-2_4523del Pathogenic ★★ same condition
DMD c.9650-4_9655del Likely pathogenic ★★ same condition
DMD p.Ala192fs 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-ser1513fs (accessed [today's date]).

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