Variant: NM_001130987.2(DYSF):c.2864+1G>A

CA1706298

443997 (ClinVar)

Gene: DYSF

Condition: autosomal recessive limb-girdle muscular dystrophy

Inheritance Mode: Autosomal recessive inheritance

UUID: a94dcf02-2341-4790-a70b-81313dbbd387

Approved on: 2025-03-06

Published on: 2025-04-04

HGVS expressions

NM_001130987.2:c.2864+1G>A
NM_001130987.2(DYSF):c.2864+1G>A
NC_000002.12:g.71568339G>A
CM000664.2:g.71568339G>A
NC_000002.11:g.71795469G>A
CM000664.1:g.71795469G>A
NC_000002.10:g.71648977G>A
NG_008694.1:g.119717G>A
ENST00000698057.1:c.236+1G>A
ENST00000258104.8:c.2810+1G>A
ENST00000410020.8:c.2864+1G>A
ENST00000258104.7:c.2810+1G>A
ENST00000394120.6:c.2813+1G>A
ENST00000409366.5:c.2813+1G>A
ENST00000409582.7:c.2861+1G>A
ENST00000409651.5:c.2906+1G>A
ENST00000409744.5:c.2771+1G>A
ENST00000409762.5:c.2861+1G>A
ENST00000410020.7:c.2864+1G>A
ENST00000410041.1:c.2864+1G>A
ENST00000413539.6:c.2903+1G>A
ENST00000429174.6:c.2810+1G>A
NM_001130455.1:c.2813+1G>A
NM_001130976.1:c.2768+1G>A
NM_001130977.1:c.2768+1G>A
NM_001130978.1:c.2810+1G>A
NM_001130979.1:c.2903+1G>A
NM_001130980.1:c.2861+1G>A
NM_001130981.1:c.2861+1G>A
NM_001130982.1:c.2906+1G>A
NM_001130983.1:c.2813+1G>A
NM_001130984.1:c.2771+1G>A
NM_001130985.1:c.2864+1G>A
NM_001130986.1:c.2771+1G>A
NM_001130987.1:c.2864+1G>A
NM_003494.3:c.2810+1G>A
NM_001130455.2:c.2813+1G>A
NM_001130976.2:c.2768+1G>A
NM_001130977.2:c.2768+1G>A
NM_001130978.2:c.2810+1G>A
NM_001130979.2:c.2903+1G>A
NM_001130980.2:c.2861+1G>A
NM_001130981.2:c.2861+1G>A
NM_001130982.2:c.2906+1G>A
NM_001130983.2:c.2813+1G>A
NM_001130984.2:c.2771+1G>A
NM_001130985.2:c.2864+1G>A
NM_001130986.2:c.2771+1G>A
NM_003494.4:c.2810+1G>A

Pathogenic

• Met criteria codes: PP4_Strong PM2_Supporting PM3 PVS1_Strong

• Not Met criteria codes: PS1

Expert Panel

Limb Girdle Muscular Dystrophy VCEP

Criteria Specification Information

Criteria Specification: ClinGen Limb Girdle Muscular Dystrophy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for DYSF Version 1.0.0

Evidence submitted by expert panel

Limb Girdle Muscular Dystrophy VCEP

The NM_003494.4: c.2810+1G>A variant in DYSF, which is also known as NM_001130987.2: c.2864+1G>A, occurs within the canonical splice donor site of intron 26. RNAseq analysis has shown that this variant disrupts splicing, resulting in skipping of DYSF exon 26 and a frameshift and premature truncation, p.(Tyr882SerfsTer4), with nonsense mediated decay predicted. Activation of an alternate splice donor site in exon 26 predicted to result in an inframe deletion of 8 amino acids, p.(Trp930_Thr937del), was also observed (PMID: 36983702; PVS1_Strong_RNA). These results are consistent with the SpliceAI predictions for this variant: score of 0.97 for donor loss and 0.57 for donor gain. This variant has been detected in at least four individuals with features of LGMD or absent dysferlin protein expression (PMID: 18853459, 26000923, 36983702, 34559919), including in a homozygous state in one individual without reported familial consanguinity (0.5 pts, PMID: 34559919) and confirmed in trans with a likely pathogenic or pathogenic variant in one individual (NM_003494.4: c.2811-20T>G, 1.0 pt, PMID: 36983702) (PM3). In the two other patients, a second DYSF variant was not identified. At least one patient with this variant and a second presumed diagnostic DYSF variant displayed progressive muscle weakness and absent dysferlin protein expression in skeletal muscle, which is highly specific for DYSF-related LGMD (PMID: 34559919; PP4_Strong). The filtering allele frequency of this variant is 0.000009455 (the upper threshold of the 95% CI of 5/111184 European (non-Finnish) exome chromosomes) in gnomAD v4.1.0, which is less than the ClinGen LGMD VCEP threshold (≤0.0001) (PM2_Supporting). Another nucleotide change at the same position, NM_003494.4: c.2810+1G>C, has also been reported in association with LGMD (PMID: 17994539). In summary, this variant meets the criteria to be classified as Pathogenic for autosomal recessive limb girdle muscular dystrophy based on the ACMG/AMP criteria applied, as specified by the ClinGen LGMD VCEP (LGMD VCEP specifications version 1.0.0; 03/06/2025): PVS1_Strong_RNA, PM3, PP4_Strong, PM2_Supporting.

Met criteria codes

• PP4_Strong: At least one patient with this variant and a second presumed diagnostic DYSF variant displayed progressive limb girdle muscle weakness and absent dysferlin protein expression in skeletal muscle, which is highly specific for DYSF-related LGMD (PMID: 34559919; PP4_Strong).
• PM2_Supporting: The filtering allele frequency of this variant is 0.000009455 (the upper threshold of the 95% CI of 5/111184 European (non-Finnish) exome chromosomes) in gnomAD v4.1.0, which is less than the ClinGen LGMD VCEP threshold (≤0.0001) (PM2_Supporting).
• PM3: This variant has been detected in at least four individuals with features of LGMD or absent dysferlin protein expression (PMID: 18853459, 26000923, 36983702, 34559919), including in a homozygous state in one individual without reported familial consanguinity (0.5 pts, PMID: 34559919) and confirmed in trans with a likely pathogenic or pathogenic variant in one individual (c.2811-20T>G, 1.0 pt, PMID: 36983702) (PM3). In the two other patients, a second DYSF variant was not identified. c.2811-20T>G can be classified as at least LP independently of their observation together: PVS1_RNA, PM2_Supporting, PS1_Moderate
• PVS1_Strong: The NM_003494.4: c.2810+1G>A variant in DYSF, which is also known as NM_001130987.2: c.2864+1G>A, occurs within the canonical splice donor site of intron 26. RNAseq analysis has shown that this variant disrupts splicing, resulting in skipping of DYSF exon 26 and a frameshift and premature truncation, p.(Tyr882SerfsTer4), with nonsense mediated decay predicted. Activation of an alternate splice donor site in exon 26 and an inframe deletion of 8 amino acids, p.(Trp930_Thr937del), was also observed (PMID: 36983702; PVS1_Strong_RNA). SpliceAI gives a score of 0.97 for donor loss and 0.57 for donor gain 21 nucleotides into exon 26, which to me looks like it would cause an inframe deletion of 7 amino acids and insertion of a cysteine, p.(Trp930_Thr937delinsCys). Exon 26 is out of frame, so skipping it would be expected to result in a frameshift and premature truncation. A patient with this variant in trans with a different splice variant expected to result in NMD showed absent dysferlin protein expression as did a patient who was homozygous, suggesting a non-significant contribution of the transcript with the inframe deletion to protein expression. Therefore, I opted to award PVS1 based on the null consequence, downgrading for an incomplete effect (PVS1_Strong_RNA) rather than emphasizing the inframe consequence (PVS1_Moderate_RNA).

Not Met criteria codes

• PS1: Another nucleotide change at this site, c.2810+1G>C, has been reported in association with LGMD (PMID: 17994539), but this variant has not yet been curated by the VCEP. The G>C change has very similar SpliceAI predictions: (0.97 for donor loss, 0.54 for donor gain at same alternative site). A maximum of PS1_Supporting could be awarded if the c.2810+1G>C variant were classified as Pathogenic, but this would not change the classification of the c.2810+1G>A variant.