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_003494.3(DYSF):c.2779del (p.Ala927Leufs)

CA233930

6685 (ClinVar)

Gene: DYSF
Condition: autosomal recessive limb-girdle muscular dystrophy
Inheritance Mode: Autosomal recessive inheritance
UUID: 6fecd0b0-0c7e-4b53-ae05-6733b8286a48
Approved on: 2025-01-08
Published on: 2025-01-08

HGVS expressions

NM_003494.3:c.2779delG
NM_003494.3(DYSF):c.2779del (p.Ala927Leufs)
NC_000002.12:g.71568307del
CM000664.2:g.71568307del
NC_000002.11:g.71795437del
CM000664.1:g.71795437del
NC_000002.10:g.71648945del
NG_008694.1:g.119685del
ENST00000698057.1:c.205del
ENST00000258104.8:c.2779del
ENST00000410020.8:c.2833del
ENST00000258104.7:c.2779del
ENST00000394120.6:c.2782del
ENST00000409366.5:c.2782del
ENST00000409582.7:c.2830del
ENST00000409651.5:c.2875del
ENST00000409744.5:c.2740del
ENST00000409762.5:c.2830del
ENST00000410020.7:c.2833del
ENST00000410041.1:c.2833del
ENST00000413539.6:c.2872del
ENST00000429174.6:c.2779del
NM_001130455.1:c.2782del
NM_001130976.1:c.2737del
NM_001130977.1:c.2737del
NM_001130978.1:c.2779del
NM_001130979.1:c.2872del
NM_001130980.1:c.2830del
NM_001130981.1:c.2830del
NM_001130982.1:c.2875del
NM_001130983.1:c.2782del
NM_001130984.1:c.2740del
NM_001130985.1:c.2833del
NM_001130986.1:c.2740del
NM_001130987.1:c.2833del
NM_003494.3:c.2779del
NM_001130987.2:c.2833del
NM_001130455.2:c.2782del
NM_001130976.2:c.2737del
NM_001130977.2:c.2737del
NM_001130978.2:c.2779del
NM_001130979.2:c.2872del
NM_001130980.2:c.2830del
NM_001130981.2:c.2830del
NM_001130982.2:c.2875del
NM_001130983.2:c.2782del
NM_001130984.2:c.2740del
NM_001130985.2:c.2833del
NM_001130986.2:c.2740del
NM_003494.4:c.2779del
More

Pathogenic

Met criteria codes 4
PP1 PP4 PM3 PVS1
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.2779del p.(Ala927LeufsTer21) variant in DYSF, which is also known as NM_001130987.2: c.2833del p.(Ala945LeufsTer21), is a frameshift variant predicted to cause a premature stop codon in biologically relevant exon 27/55 leading to nonsense mediated decay in a gene in which loss of function is an established disease mechanism (PVS1). This variant has been detected in at least 13 individuals with limb girdle muscular dystrophy. Of those individuals, one was compound heterozygous for the variant and a pathogenic variant (c.857T>A (p.Val286Glu), 1.0 pt, PMID: 18832576), and 10 were homozygous (0.75 pts, PMID: 16010686, 17825554) (PM3). 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: 18832576, 17825554). The variant was also reported to co-segregate with the disease in 10 affected family members and has been described as a founder variant among Jews of the Caucus region, with an estimated carrier frequency of 4% (PP1 (capped with PP4_Strong); PMID: 17825554). The filtering allele frequency of the variant is 0.0006 for Admixed American genome alleles in gnomAD v3.1.2 (the upper threshold of the 95% CI of 4/15288), 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, PM3, PP4_Strong, PP1.
Met criteria codes
PP1
The variant was also reported to co-segregate with the disease in 10 affected family members and has been described as a founder variant among Jews of the Caucus region, with an estimated carrier frequency of 4% (PP1; PMID: 17825554). (capped with PP4_Strong)
PP4
At least one patient with this variant displayed progressive weakness and absent dysferlin protein expression, which is highly specific for DYSF-associated LGMD (PP4_Strong, PMID: 18832576, 17825554).
PM3
This variant has been detected in at least 13 individuals with limb girdle muscular dystrophy. Of those individuals, one was compound heterozygous for the variant and a pathogenic variant (c.857T>A (p.Val286Glu), 1.0 pt, PMID: 18832576), and 10 were homozygous (0.75 pts, PMID: 16010686, 17825554) (PM3).
PVS1
The NM_003494.4: c.2779del p.(Ala927LeufsTer21) variant in DYSF, which is also known as NM_001130987.2: c.2833del p.(Ala945LeufsTer21), is a frameshift variant predicted to cause a premature stop codon in biologically relevant exon 27/55 leading to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism (PVS1).
Not Met criteria codes
PM2
The filtering allele frequency of the variants is 0.0006 for Admixed American genome alleles in gnomAD v3.1.2 (the upper threshold of the 95% CI of 4/15288), which is greater than the LGMD VCEP threshold (<0.0001) for PM2_Supporting (criterion not met).
Curation History
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