DYSF p.Thr899Pro

The NM_003494.4: c.2641A>C variant in DYSF, which is also known as NM_001130987.2: c.2695A>C p.(Thr899Pro), is a missense variant predicted to cause substitution of threonine to proline at amino acid 881, p.(Thr881Pro). This variant has been observed in at least three individuals with suspected LGMD, including with a second pathogenic variant in unknown phase in two patients (NM_003494.4: c.907-3C>A, 0.5 pts, PMID: 24488599; c.4756C>T p.(Arg1586Ter), 0.5 pts, PMID: 30564623; LOVD Individual #00221032; PM3). At least one patient with this variant and a second pathogenic DYSF variant had both clinical features of LGMD and absent dysferlin expression in muscle or blood monocytes, which is highly specific for DYSF-related LGMD (PMID: 33927379, 24488599; PP4_Strong). The highest population allele frequency for this variant in gnomAD v4.1.0 is 0.00001667 (1/59986 Admixed American chromosomes), which is less than the threshold of 0.0001 for PM2_Supporting, meeting this criterion (PM2_Supporting). The computational predictor REVEL gives a score of 0.74, which is above the LGMD VCEP threshold of ≥0.70, evidence that correlates with impact to DYSF function (PP3). This variant affects the last amino acid of exon 25, at the -3 position of the splice donor. Splice AI does not predict it will affect splicing, though a mini-gene assay has demonstrated that it results in partial skipping of exon 25, causing an in-frame deletion (PMID: 25312915; PVS1_RNA_Moderate not met). Immunofluorescence and 2-A assays of dysferlin membrane localization in HEK293T cells showed conflicting results for the Thr881Pro protein, which was classified as functional by 2-A assay but non-functional by immunofluorescence assay (PMID: 35028538; PS3_Moderate not met). In summary, this variant is classified as Likely Pathogenic for autosomal recessive limb girdle muscular dystrophy based on the ACMG/AMP criteria applied, as specified by the ClinGen LGMD VCEP (specifications v2.0.0; 04/30/2026): PM3, PP4_Strong, PP3, PM2_Supporting.