Evidence Repository
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.2402C>T (p.Ala801Val)

CA1706139

288008 (ClinVar)

Gene: DYSF (HGNC:8291)
Condition: autosomal recessive limb-girdle muscular dystrophy (MONDO:0015152)
Inheritance Mode: Autosomal recessive inheritance
UUID: b02c22a7-4e54-4755-aae6-73cce8a45c16
Approved on: 2026-01-23
Published on: 2026-02-17

HGVS expressions

NM_001130987.2:c.2402C>T
NM_001130987.2(DYSF):c.2402C>T (p.Ala801Val)
NC_000002.12:g.71561937C>T
CM000664.2:g.71561937C>T
NC_000002.11:g.71789067C>T
CM000664.1:g.71789067C>T
NC_000002.10:g.71642575C>T
NG_008694.1:g.113315C>T
ENST00000258104.8:c.2348C>T
ENST00000410020.8:c.2402C>T
ENST00000258104.7:c.2348C>T
ENST00000394120.6:c.2351C>T
ENST00000409366.5:c.2351C>T
ENST00000409582.7:c.2399C>T
ENST00000409651.5:c.2444C>T
ENST00000409744.5:c.2309C>T
ENST00000409762.5:c.2399C>T
ENST00000410020.7:c.2402C>T
ENST00000410041.1:c.2402C>T
ENST00000413539.6:c.2441C>T
ENST00000429174.6:c.2348C>T
NM_001130455.1:c.2351C>T
NM_001130976.1:c.2306C>T
NM_001130977.1:c.2306C>T
NM_001130978.1:c.2348C>T
NM_001130979.1:c.2441C>T
NM_001130980.1:c.2399C>T
NM_001130981.1:c.2399C>T
NM_001130982.1:c.2444C>T
NM_001130983.1:c.2351C>T
NM_001130984.1:c.2309C>T
NM_001130985.1:c.2402C>T
NM_001130986.1:c.2309C>T
NM_001130987.1:c.2402C>T
NM_003494.3:c.2348C>T
NM_001130455.2:c.2351C>T
NM_001130976.2:c.2306C>T
NM_001130977.2:c.2306C>T
NM_001130978.2:c.2348C>T
NM_001130979.2:c.2441C>T
NM_001130980.2:c.2399C>T
NM_001130981.2:c.2399C>T
NM_001130982.2:c.2444C>T
NM_001130983.2:c.2351C>T
NM_001130984.2:c.2309C>T
NM_001130985.2:c.2402C>T
NM_001130986.2:c.2309C>T
NM_003494.4:c.2348C>T
More

Likely Benign

Met criteria codes 1
BS1
Not Met criteria codes 4
PS3 BP4 PP3 PM3

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 2.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Limb Girdle Muscular Dystrophy VCEP
The NM_003494.4: c.2348C>T variant in DYSF, which is also known as NM_001130987.2: c.2402C>T p.(Ala801Val), is a missense variant predicted to cause substitution of alanine to valine at amino acid 801, p.(Ala801Val). This variant has been observed in at least three individuals with suspected LGMD in a heterozygous state, but none of them would be scoreable for PM3 application (PMID: 30564623, Jain Foundation Dysferlin Registry internal data communication; PM3_supporting not met). The filtering allele frequency of this variant is 0.001406 (the lower threshold of the 95% CI of 123/74924 African/African American chromosomes) in gnomAD v4.1.0, which is greater than the LGMD VCEP BS1 threshold (>0.001) (BS1 met). The computational predictor REVEL gives a score of 0.28 (PP3 and BP4 not met). In summary, this variant is classified as likely benign 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; 01/23/2026): BS1.
Met criteria codes
BS1
The filtering allele frequency of this variant is 0.001406 (the lower threshold of the 95% CI of 123/74924 African/African American chromosomes) in gnomAD v4.1.0, which is greater than the LGMD VCEP BS1 threshold (>0.001) (BS1 met).
Not Met criteria codes
PS3
Not in Tominaga et al. paper and no other functional studies.
BP4
The computational predictor REVEL gives a score of 0.28 (PP3 and BP4 not met).
PP3
The computational predictor REVEL gives a score of 0.28 (PP3 and BP4 not met). Splice AI; 0.05
PM3
This variant has been observed in at least three individuals with suspected LGMD in a heterozygous state, but none of them would be scoreable for PM3 application (PMID: 30564623, Jain Foundation Dysferlin Registry internal data communication; PM3_supporting not met).
Curation History
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