Is DYSF p.Pro15fs (c.42_43del) pathogenic?

DYSF p.Pro15fs (c.4243del) is classified Likely pathogenic in DYSF (ClinVar, Single submitter, 1 submitter; last evaluated 2023-03-23). Absent from gnomAD; Associated with Miyoshi muscular dystrophy 1.

What condition is associated with DYSF p.Pro15fs (c.42_43del)?

DYSF p.Pro15fs (c.42_43del) is associated with Miyoshi muscular dystrophy 1 (ClinVar).

How common is DYSF p.Pro15fs (c.42_43del) in the general population?

DYSF p.Pro15fs (c.42_43del) is absent from gnomAD (gnomAD).

How is Miyoshi myopathy inherited?

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

DYSF p.Pro15fs

c.42_43del · rs2466863398 · VCV2674985

Likely pathogenic Single submitter

Classification

Likely 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

Miyoshi muscular dystrophy 1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function; NMD-escape possible for C-terminal truncations
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 1.1	GERP -0.74, phastCons 0.99

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: DYSF
Protein: p.Pro15fs
Coding: c.42_43del
MANE Select: NM_001130987 · reported on NM_003494
dbSNP: rs2466863398
Type: Microsatellite
Location: chr2:71454035 (GRCh38)
Gene constraint: LOEUF 0.836 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 79.25 · 11 PDB
Residue 15: a β-strand; the c2 1 domain

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

Disease context

Miyoshi muscular dystrophy 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Miyoshi myopathy (Orphanet):

Inheritance: Autosomal recessive
Onset: Adult
Prevalence: 1-9 / 1 000 000 (Japan)

Similar variants

DYSF p.Leu1092fs Pathogenic ★★★ same condition
DYSF p.Phe1128fs Pathogenic ★★★ same condition
DYSF p.Ser1939fs Pathogenic ★★★ same condition
DYSF p.1080AE[3] Benign ★★★ same condition
DYSF p.Leu298fs Pathogenic ★★ same condition
DYSF p.Ser1189fs Pathogenic ★★ same condition
DYSF p.2087ILFI[1] Uncertain significance ★★ same condition
DYSF p.His1055fs 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/dysf-p-pro15fs (accessed [today's date]).

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