Is DYSF p.Ala829= (c.2487C>T) pathogenic?

DYSF p.Ala829= (c.2487C>T) is classified Likely benign in DYSF (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-05-01). Very rare (popmax 0.000339%, nfe); Associated with neuromuscular disease caused by qualitative or quantitative defects of dysferlin.

How common is DYSF p.Ala829= (c.2487C>T) in the general population?

DYSF p.Ala829= (c.2487C>T) is very rare (popmax 0.000339%, nfe) (gnomAD).

DYSF p.Ala829=

Q: What condition is associated with DYSF p.Ala829= (c.2487C>T)?

DYSF p.Ala829= (c.2487C>T) is associated with neuromuscular disease caused by qualitative or quantitative defects of dysferlin (ClinVar).

c.2487C>T · rs1199331931 · VCV798435

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.000339%, nfe)

Conditions

neuromuscular disease caused by qualitative or quantitative defects of dysferlin

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.29	GERP -3.5, phastCons 0.12
Overall
CADD	7.838	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000339% European (non-Finnish) · 4/1,180,058 alleles

Filtering AF 7.9e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 5.4e-05%

Overall 0.000248% 4/1,614,164 alleles · very rare exomes 2/1,461,894 · genomes 2/152,270 · joint denominator

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.Ala829=
Coding: c.2487C>T
MANE Select: NM_001130987
dbSNP: rs1199331931
Type: single nucleotide variant
Location: chr2:71564135 (GRCh38)
Gene constraint: LOEUF 0.836 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 79.25 · 11 PDB
Residue 829: a turn

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

Disease context

neuromuscular disease caused by qualitative or quantitative defects of dysferlin — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

DYSF p.Ala829Val Uncertain significance ★★ ⚠ same residue
DYSF p.Ala829Thr Conflicting classifications of pathogenicity ★ ⚠ same residue
DYSF p.Ala829fs Pathogenic ★ same residue
DYSF p.Ala829Ser 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

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-ala829 (accessed [today's date]).

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