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_000023.4(SGCA):c.241C>T (p.Arg81Cys)

CA220233

92302 (ClinVar)

Gene: SGCA (HGNC:6442)
Condition: autosomal recessive limb-girdle muscular dystrophy (MONDO:0015152)
Inheritance Mode: Autosomal recessive inheritance
UUID: 7327f277-2ca2-4559-8b16-f6da816a8148
Approved on: 2025-01-09
Published on: 2025-01-09

HGVS expressions

NM_000023.4(SGCA):c.241C>T (p.Arg81Cys)
NM_000023.4:c.241C>T
NC_000017.11:g.50167665C>T
CM000679.2:g.50167665C>T
NC_000017.10:g.48245026C>T
CM000679.1:g.48245026C>T
NC_000017.9:g.45600025C>T
NG_008889.1:g.6661C>T
ENST00000504073.2:c.241C>T
ENST00000511303.6:n.38-282C>T
ENST00000512526.2:c.241C>T
ENST00000682109.1:c.121C>T
ENST00000683294.1:c.241C>T
ENST00000262018.8:c.241C>T
ENST00000262018.7:c.241C>T
ENST00000344627.10:c.241C>T
ENST00000502555.5:c.157+178C>T
ENST00000511303.5:c.34-282C>T
ENST00000512526.1:c.85C>T
ENST00000513821.5:c.241C>T
ENST00000513942.5:n.104-282C>T
ENST00000514934.1:c.*18+178C>T
NM_000023.2:c.241C>T
NM_001135697.1:c.241C>T
NM_000023.3:c.241C>T
NM_001135697.2:c.241C>T
NR_135553.1:n.297C>T
NM_001135697.3:c.241C>T
NR_135553.2:n.277C>T
More

Likely Pathogenic

Met criteria codes 5
PM2_Supporting PP4_Strong PP1 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 SGCA 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_000023.4: c.241C>T variant in SGCA is a missense variant predicted to cause substitution of arginine by cysteine at amino acid 81 (p.Arg81Cys). This variant has been detected in at least three individuals with symptoms of limb girdle muscular dystrophy, including confirmed in trans with a pathogenic or likely pathogenic variant (c.850C>T p.(Arg284Cys), 1.0 pt, PMID: 17994539) and in a homozygous state in two patients (0.75 pts, PMID: 31069529, 30345904) (PM3). At least one patient with this variant and a second presumed diagnostic SGCA variant displayed progressive limb girdle muscle weakness and significantly reduced or absent alpha-sarcoglycan protein expression, which is highly specific for SGCA-related LGMD (PP4_Strong; PMID: 17994539, 26404900; LOVD Individual #00133411). In addition, the variant has been reported to segregate with autosomal recessive limb girdle muscular dystrophy in one affected family member (PP1; PMID: 17994539). The highest population minor allele frequency in gnomAD v2.1.1 is 0.00003 (1/30576 alleles) in the South Asian population, which is lower than the ClinGen LGMD VCEP threshold (0.00009) for PM2_Supporting, meeting this criterion (PM2_Supporting). The computational predictor REVEL gives a score of 0.934, which is above the threshold of 0.7, evidence that correlates with impact to SGCA 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; 01/09/2025): PP4_Strong, PM3, PP1, PP3, PM2_Supporting.
Met criteria codes
PM2_Supporting
The highest population minor allele frequency in gnomAD v2.1.1 is 0.00003 (1/30576 alleles) in the South Asian population, which is lower than the ClinGen LGMD VCEP threshold (0.00009) for PM2_Supporting, meeting this criterion (PM2_Supporting).
PP4_Strong
At least one patient with this variant and a second SGCA variant displayed progressive limb girdle muscle weakness and significantly reduced or absent alpha sarcoglycan protein expression, which is highly specific for SGCA-related LGMD (PP4_Strong; PMID: 17994539).
PP1
The variant has been reported to segregate with autosomal recessive limb girdle muscular dystrophy in one affected family member (PP1; PMID: 17994539).
PP3
The computational predictor REVEL gives a score of 0.934, which is above the threshold of 0.7, evidence that correlates with impact to SGCA function (PP3).
PM3
This variant has been detected in at least 3 individuals with autosomal recessive limb girdle muscular dystrophy, including confirmed in trans with a pathogenic or likely pathogenic variant (c.850C>T p.(Arg284Cys), 1.0 pt, PMID: 17994539) and in a homozygous state in two patients (0.75 pts, PMID: 31069529, 30345904) (PM3).
Curation History
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