The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computed assertion could be determined for this classification!


Variant: NM_001130987.2(DYSF):c.951+1del

CA253921

6684 (ClinVar)

Gene: DYSF
Condition: autosomal recessive limb-girdle muscular dystrophy
Inheritance Mode: Autosomal recessive inheritance
UUID: 893c0a55-bb7e-44b1-98d2-d451b50068dc
Approved on: 2025-01-08
Published on: 2025-01-08

HGVS expressions

NM_001130987.2:c.951+1del
NM_001130987.2(DYSF):c.951+1del
NC_000002.12:g.71516243del
CM000664.2:g.71516243del
NC_000002.11:g.71743373del
CM000664.1:g.71743373del
NC_000002.10:g.71596881del
NG_008694.1:g.67621del
ENST00000258104.8:c.855+1del
ENST00000410020.8:c.951+1del
ENST00000258104.7:c.855+1del
ENST00000394120.6:c.858+1del
ENST00000409366.5:c.858+1del
ENST00000409582.7:c.948+1del
ENST00000409651.5:c.951+1del
ENST00000409744.5:c.858+1del
ENST00000409762.5:c.948+1del
ENST00000410020.7:c.951+1del
ENST00000410041.1:c.951+1del
ENST00000413539.6:c.948+1del
ENST00000429174.6:c.855+1del
NM_001130455.1:c.858+1del
NM_001130976.1:c.855+1del
NM_001130977.1:c.855+1del
NM_001130978.1:c.855+1del
NM_001130979.1:c.948+1del
NM_001130980.1:c.948+1del
NM_001130981.1:c.948+1del
NM_001130982.1:c.951+1del
NM_001130983.1:c.858+1del
NM_001130984.1:c.858+1del
NM_001130985.1:c.951+1del
NM_001130986.1:c.858+1del
NM_001130987.1:c.951+1del
NM_003494.3:c.855+1del
NM_001130455.2:c.858+1del
NM_001130976.2:c.855+1del
NM_001130977.2:c.855+1del
NM_001130978.2:c.855+1del
NM_001130979.2:c.948+1del
NM_001130980.2:c.948+1del
NM_001130981.2:c.948+1del
NM_001130982.2:c.951+1del
NM_001130983.2:c.858+1del
NM_001130984.2:c.858+1del
NM_001130985.2:c.951+1del
NM_001130986.2:c.858+1del
NM_003494.4:c.855+1del
More

Pathogenic

Met criteria codes 4
PVS1 PP4_Strong PM3_Strong PP1
Not Met criteria codes 1
PM2

Evidence Links 0

Expert Panel

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

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Limb Girdle Muscular Dystrophy VCEP
The NM_003494.4: c.855+1del variant in DYSF, which is also known as NM_001130987.2: c.951+1del, occurs within the canonical splice donor site of intron 8. It is predicted to cause skipping of biologically relevant exon 8/55, resulting in an in-frame deletion of 21 amino acids (PVS1_Moderate). RNAseq data has confirmed that this variant results in in aberrant splicing, suggesting use of an alternative acceptor site that deletes the first basepair of DYSF exon 9 and leads to a frameshift and premature truncation p.(Val286TrpfsTer2) (PMID: 36983702). This variant has been detected in at least 12 individuals with limb girdle muscular dystrophy (PMID: 20544924, 17828519, 18853459, 36983702). Of those individuals, at least two were compound heterozygous for the variant and a pathogenic variant (c.3504dup p.(Lys1169GlnfsTer6), 1.0 pt, PMID: 20544924; c.3126G>A p.(Trp1024Ter): 1.0 pt, PMID: 18853459), and at least one was homozygous (0.25 pts, PMID: 18853459) (PM3_Strong). At least one patient with this variant displayed progressive limb-girdle muscle weakness and absent dysferlin protein expression, which is highly specific for DYSF-associated LGMD (PP4_Strong, PMID: 18853459, 36983702). The variant was also reported to co-segregate with the disease in two affected family members from two families (PMID: 18853459) (PP1, capped with PP4_Strong). The filtering allele frequency of the variant is 0.0009441 for Admixed American genome alleles in gnomAD v3.1.2 (the upper threshold of the 95% CI of 8/15286), which is greater than the LGMD VCEP threshold (<0.0001) for PM2_Supporting (criterion not met). 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; 01/08/2025): PVS1_Moderate, PM3_Strong, PP4_Strong, PP1.
Met criteria codes
PVS1
The NM_003494.4: c.855+1del variant in DYSF, which is also known as NM_001130987.2: c.951+1del, occurs within the canonical splice donor site (+/- 1,2) of intron 8. RNAseq data has confirmed that this variant results in aberrant splicing, suggesting use of an alternative acceptor site that deletes the first basepair of DYSF exon 9 and leads to a frameshift and premature truncation p.(Val286TrpfsTer2) (PMID: 36983702) (PVS1_RNA).
PP4_Strong
At least one patient with this variant displayed progressive limb-girdle muscle weakness and absent dysferlin protein expression, which is highly specific for DYSF-associated LGMD (PP4_Strong, PMID: 18853459, 36983702).
PM3_Strong
This variant has been detected in at least 12 individuals with limb girdle muscular dystrophy (PMID: 20544924, 17828519, 18853459, 36983702). Of those individuals, at least two were compound heterozygous for the variant and a pathogenic variant (c.3504dup p.(Lys1169GlnfsTer6), 1.0 pt, PMID: 20544924; c.3126G>A p.(Trp1024Ter): 1.0 pt, PMID: 18853459), and at least one was homozygous (0.25 pts, PMID: 18853459) (PM3_Strong).
PP1
The variant was reported to co-segregate with the disease in two affected family members from two families (PMID: 18853459) (PP1). (capped with PP4_strong)
Not Met criteria codes
PM2
The filtering allele frequency of the variants is 0.0009441 for Admixed American genome alleles in gnomAD v3.1.2 (the upper threshold of the 95% CI of 8/15286), which is greater than the LGMD VCEP threshold (<0.0001) for PM2_Supporting (criterion not met).
Curation History
The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. If you have questions about the information contained on this website, please see a health care professional.
¤ Powered by BCM's Genboree.