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_000232.5(SGCB):c.265G>A (p.Val89Met)

CA2918446

551805 (ClinVar)

Gene: SGCB
Condition: autosomal recessive limb-girdle muscular dystrophy
Inheritance Mode: Autosomal recessive inheritance
UUID: f98879f1-c7ae-43f8-9b74-3c53efca968b
Approved on: 2025-01-08
Published on: 2025-01-08

HGVS expressions

NM_000232.5:c.265G>A
NM_000232.5(SGCB):c.265G>A (p.Val89Met)
NC_000004.12:g.52029842C>T
CM000666.2:g.52029842C>T
NC_000004.11:g.52896008C>T
CM000666.1:g.52896008C>T
NC_000004.10:g.52590765C>T
NG_008891.1:g.13478G>A
ENST00000381431.10:c.265G>A
ENST00000381431.9:c.265G>A
ENST00000506357.5:c.348G>A
ENST00000514133.1:c.342G>A
NM_000232.4:c.265G>A
More

Likely Pathogenic

Met criteria codes 5
PM2_Supporting PM3_Strong PP1 PP4 PP3

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 SGCB 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_000232.5: c.265G>A variant in SGCB is a missense variant predicted to cause substitution of valine by methionine at amino acid 89 (p.Val89Met). This variant has been detected in at least four individuals with symptoms of limb girdle muscular dystrophy. Of those individuals, one was compound heterozygous for the variant and a pathogenic variant (c.391C>T p.(Arg131Ter), 1 pt, ClinVar SCV000748307.5 internal data communication), and three patients were homozygous for the variant (1 pt, PMID: 28889091, 30838351, 29797799) (PM3_Strong). At least one of these patients displayed progressive limb girdle muscle weakness (PP4). This variant was also shown to co-segregate with autosomal recessive LGMD in one affected family member (PMID: 28889091; PP1). The highest population minor allele frequency in gnomAD v2.1.1 is 0.00003 in the Admixed American population (1/34588 exome alleles), which is lower than the LGMD VCEP threshold (<0.00009) for PM2_Supporting, meeting this criterion (PM2_Supporting). The computational predictor REVEL gives a score of 0.932, which is above the threshold of 0.7, evidence that correlates with impact to SGCB function (PP3). In summary, this variant meets the criteria to be 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 (LGMD VCEP specifications version 1.0.0; 01/08/2025): PM3_Strong, PP4, PM2_Supporting, PP3, PP1.
Met criteria codes
PM2_Supporting
The highest population minor allele frequency in gnomAD v2.1.1 is 0.00003 (1/34588 exome alleles) in the Admixed American population, which is lower than the ClinGen Limb-Girdle Muscular Dystrophy threshold (<0.00009) for PM2_Supporting, meeting this criterion (PM2_Supporting).
PM3_Strong
This variant has been detected in at least four individuals with autosomal recessive limb girdle muscular dystrophy. Of those individuals, one was compound heterozygous for the variant and a pathogenic variant (c.391C>T p.(Arg131Ter), 1 pt, SCV000748307.5 internal data communication), and three patients were homozygous for the variant (1 pt, PMID: 28889091, 30838351, 29797799) (PM3_Strong).
PP1
This variant was shown to co-segregate with autosomal recessive LGMD in one affected family member (PMID: 28889091).
PP4
At least one patient with this variant and a second presumed diagnostic variant in SGCB displayed progressive limb girdle muscle weakness (PP4). ARC note: all SGC genes screened in Yis et al. patient but "deficient" provides insufficient detail about magnitude of reduction. Cannot confirm all SGC genes screened in GeneDx patient though it seems likely.
PP3
The computational predictor REVEL gives a score of 0.932, which is above the threshold of 0.7, evidence that correlates with impact to SGCB function (PP3).
Curation History
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