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
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Variant: NM_000232.5(SGCB):c.452C>G (p.Thr151Arg)

CA119849

8712 (ClinVar)

Gene: SGCB
Condition: autosomal recessive limb-girdle muscular dystrophy
Inheritance Mode: Autosomal recessive inheritance
UUID: 4e43b5fa-2280-41ca-9107-05d165133751
Approved on: 2025-01-09
Published on: 2025-01-09

HGVS expressions

NM_000232.5:c.452C>G
NM_000232.5(SGCB):c.452C>G (p.Thr151Arg)
NC_000004.12:g.52028899G>C
CM000666.2:g.52028899G>C
NC_000004.11:g.52895065G>C
CM000666.1:g.52895065G>C
NC_000004.10:g.52589822G>C
NG_008891.1:g.14421C>G
ENST00000381431.10:c.452C>G
ENST00000381431.9:c.452C>G
ENST00000506357.5:c.535C>G
ENST00000514133.1:c.529C>G
NM_000232.4:c.452C>G
More

Pathogenic

Met criteria codes 6
PP1_Moderate PM2_Supporting PP4 PP3 PS3_Moderate PM3_Strong

Evidence Links 1

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.452C>G variant in SGCB is a missense variant predicted to cause substitution of threonine by arginine at amino acid 151 p.(Thr151Arg). This variant has been detected in at least five individuals with signs of limb girdle muscular dystrophy, including in a homozygous state (1.0 pt; PMID: 30564623, 21480868, 7581448) and confirmed in trans with a pathogenic variant (c.271C>T p.(Arg91Cys), 1.0 pt, PMID: 9565988) (PM3_Strong). At least one patient with this variant was clinically suspected to have limb girdle muscular dystrophy (PP4). The variant has also been shown to segregate with autosomal recessive LGMD in at least 5 affected family members in families from the Plain community in southern Indiana and has been proposed as a founder variant for this population (PP1_Moderate; PMID: 7581448, 9565988, 28615891, 3083835). The minor allele frequency of this variant is 0.00006498 for European (non-Finnish) chromosomes in gnomAD v2.1.1 (1/15390), which is lower than the LGMD VCEP threshold (<0.00009) for PM2_Supporting, and therefore meets this criterion (PM2_Supporting). In vitro assays of membrane localization in HEK293 and HER-911 cells showed that expression of p.Thr151Arg in β-sarcoglycan disrupted localization of both the β-sarcoglycan subunit and the sarcoglycan complex to the plasma membrane, indicating an impact of the variant on protein function (PMID: 37317968, 22095924) (PS3_Moderate). The computational predictor REVEL gives a score of 0.87, which is above the LGMD VCEP threshold of 0.70, evidence that correlates with impact to SGCB function (PP3). 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; 01/09/2025): PM3_Strong, PP4, PP1_Moderate, PM2_Supporting, PS3_Moderate, PP3.
Met criteria codes
PP1_Moderate
The variant has been reported to segregate with LGMD in at least 5 affected family members in families from the Plain community in southern Indiana and has been proposed as a founder variant for this population (PP1_Moderate; PMID: 7581448, 9565988, 28615891, 3083835).
PM2_Supporting
The minor allele frequency of this variant is 0.00006498 for European (non-Finnish) chromosomes in gnomAD v2.1.1 (1/15390), which is lower than the LGMD VCEP threshold (<0.00009) for PM2_Supporting, and therefore meets this criterion (PM2_Supporting).
PP4
At least one patient with this variant was clinically suspected to have limb girdle muscular dystrophy (PP4).
PP3
The computational predictor REVEL gives a score of 0.87, which is above the LGMD VCEP threshold of 0.70, evidence that correlates with impact to SGCB function (PP3).
PS3_Moderate
In vitro assays of membrane localization in HEK293 and HER-911 cells showed that expression of p.Thr151Arg in β-sarcoglycan disrupted localization of both the β-sarcoglycan subunit and the sarcoglycan complex to the plasma membrane, indicating an impact of the c.452C>G p.(Thr151Arg) variant on protein function (PMID: 37317968, 22095924) (PS3_Moderate).

PM3_Strong
This variant has been detected in at least five individuals with signs of limb girdle muscular dystrophy, including in a homozygous state (1.0 pt; PMID: 30564623, 21480868, 7581448) and confirmed in trans with a pathogenic variant (c.271C>T p.(Arg91Cys), 1.0 pt, PMID: 9565988) (PM3_Strong).
Curation History
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