Is DYSF p.Arg600Trp (c.1798C>T) pathogenic?

DYSF p.Arg600Trp (c.1798C>T) is classified Conflicting classifications of pathogenicity in DYSF (ClinVar, Conflicting submitters, 8 submitters; last evaluated 2025-07-20). AlphaMissense: likely benign (0.2457); Ultra-rare (popmax 0.0189%, amr); Associated with Miyoshi muscular dystrophy 1.

How common is DYSF p.Arg600Trp (c.1798C>T) in the general population?

DYSF p.Arg600Trp (c.1798C>T) is ultra-rare (popmax 0.0189%, amr) (gnomAD).

How is Miyoshi myopathy inherited?

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

What do computational predictors say about DYSF p.Arg600Trp (c.1798C>T)?

AlphaMissense predicts likely benign (score 0.2457) — an in-silico prediction, not a clinical call.

DYSF p.Arg600Trp

Q: What condition is associated with DYSF p.Arg600Trp (c.1798C>T)?

DYSF p.Arg600Trp (c.1798C>T) is associated with Miyoshi muscular dystrophy 1, autosomal recessive limb-girdle muscular dystrophy type 2B, neuromuscular disease caused by qualitative or quantitative defects of dysferlin (ClinVar).

c.1798C>T · rs149386446 · VCV498346

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 8 submitters

AlphaMissense

likely benign

0.2457 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0189%, amr)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Miyoshi muscular dystrophy 1

Computational evidence

Protein change
AlphaMissense	0.2457	likely benign
REVEL	0.599	indeterminate
SaProt	LLR -8.55	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4	GERP 0.78, phastCons 1
Regional constraint	o/e 1.02	unconstrained · MANE · 85 kb · p 0.54 · regional, not allelic
Overall
CADD	25.1	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM R582W vs ClinVar R600W) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0189% Admixed American · 11/58,340 alleles

Filtering AF 0.0139% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0133%

Overall 0.0142% 228/1,605,250 alleles · ultra-rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0189%	5,304
African / African-American	0.0187%	5,352
European (non-Finnish)	0.0159%	6,297
East Asian	0.0135%	7,414
Remaining individualsnot grpmax-eligible	0.0112%	8,896
South Asian	0.00338%	29,626

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: DYSF
Protein: p.Arg600Trp
Coding: c.1798C>T
MANE Select: NM_001130987
dbSNP: rs149386446
Type: single nucleotide variant
Location: chr2:71551712 (GRCh38)
Gene constraint: LOEUF 0.836 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 79.25 · 11 PDB
Residue 600: a β-strand

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

Also linked: autosomal recessive limb-girdle muscular dystrophy type 2B neuromuscular disease caused by qualitative or quantitative defects of dysferlin

For Miyoshi myopathy (Orphanet):

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

Similar variants

DYSF p.Arg600Leu Benign ★★★ same residue
DYSF p.Arg600Gln Likely benign ★ same residue
DYSF p.Arg600= Uncertain significance same residue
DYSF c.1003-3C>A Pathogenic ★★★ same condition
DYSF c.1033+1G>A Pathogenic ★★★ same condition
DYSF c.1033+4A>T Likely pathogenic ★★★ same condition
DYSF c.1149+1G>A Pathogenic ★★★ same condition
DYSF c.1149+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/dysf-p-arg600trp (accessed [today's date]).

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