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.229C>T (p.Arg77Cys)

CA120427

9437 (ClinVar)

Gene: SGCA
Condition: autosomal recessive limb-girdle muscular dystrophy
Inheritance Mode: Autosomal recessive inheritance
UUID: 932947fc-e18c-4bdf-a0d3-cd7109c13457
Approved on: 2025-01-08
Published on: 2025-01-08

HGVS expressions

NM_000023.4:c.229C>T
NM_000023.4(SGCA):c.229C>T (p.Arg77Cys)
NC_000017.11:g.50167653C>T
CM000679.2:g.50167653C>T
NC_000017.10:g.48245014C>T
CM000679.1:g.48245014C>T
NC_000017.9:g.45600013C>T
NG_008889.1:g.6649C>T
ENST00000504073.2:c.229C>T
ENST00000511303.6:n.38-294C>T
ENST00000512526.2:c.229C>T
ENST00000682109.1:c.109C>T
ENST00000683294.1:c.229C>T
ENST00000262018.8:c.229C>T
ENST00000262018.7:c.229C>T
ENST00000344627.10:c.229C>T
ENST00000502555.5:c.157+166C>T
ENST00000511303.5:c.34-294C>T
ENST00000512526.1:c.73C>T
ENST00000513821.5:c.229C>T
ENST00000513942.5:n.104-294C>T
ENST00000514934.1:c.*18+166C>T
NM_000023.2:c.229C>T
NM_001135697.1:c.229C>T
NM_000023.3:c.229C>T
NM_001135697.2:c.229C>T
NR_135553.1:n.285C>T
NM_001135697.3:c.229C>T
NR_135553.2:n.265C>T
More

Pathogenic

Met criteria codes 5
PP4 PP3 PS3_Supporting PM3_Strong PP1_Strong
Not Met criteria codes 21
BP5 BP7 BP2 BP3 BP4 BP1 PS2 PS4 PS1 PP2 PM6 PM2 PVS1 PM1 PM4 PM5 BA1 BS2 BS4 BS3 BS1

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.229C>T variant in SGCA is a missense variant predicted to cause substitution of arginine by cysteine at amino acid 77 (p.Arg77Cys). This variant has been detected in at least 12 individuals with symptoms of limb girdle muscular dystrophy. Of those individuals, two were confirmed compound heterozygous for the variant and a pathogenic or likely pathogenic variant (c.850C>T, 2 pts, PMID: 12566530, LOVD Individual #0000223892), and at least two were homozygous for the variant (1 pt, PMID: 12566530, 23989969, 7663524, 37628638) (PM3_Strong). The variant has been reported to segregate with autosomal recessive limb girdle muscular dystrophy in 10 affected family members from five families (PP1_Strong; LOVD Individual #0000223892, PMID: 12566530, 7663524). At least one patient with this variant displayed progressive limb girdle muscle weakness and reduced alpha-sarcoglycan protein expression, which is highly specific for SGCA-related LGMD (PMID: 7663524; PP4) (capped with PP1_Strong). The filtering allele frequency of this variant is 0.0004392 (the lower threshold of the 95% CI of 62/112872 exome chromosomes) in the European (non-Finnish) population in gnomAD v2.1.1, which is lower than the ClinGen LGMD VCEP threshold (>0.0009) for BS1 (BS1, PM2_Supporting not met). In vitro assays have demonstrated this variant disrupts membrane localization of the sarcoglycan protein complex (PMID: 18535179; PS3_Supporting), and the computational predictor REVEL gives a score of 0.95, which exceeds the threshold of ≥0.70, evidence that correlates with impact to SGCA 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; 01/08/2025): PM3_Strong, PP1_Strong, PP4, PP3, PS3_Supporting.
Met criteria codes
PP4
At least one patient with this variant displayed progressive limb girdle muscle weakness and reduced alpha-sarcoglycan protein expression, which is highly specific for SGCA-related LGMD (PMID: 7663524; PP4) (capped with PP1_Strong).
PP3
The computational predictor REVEL gives a score of 0.95, which exceeds the threshold of ≥0.70, evidence that correlates with impact to SGCA function (PP3).
PS3_Supporting
Confocal immunofluorescence in permeabilized βγδ-HEK cells showed the formation of intracellular aggregates by the R77C mutant, which does not localize with the other sarcoglycans and remains trapped in the Endoplasmic Reticulum (EM), indicating that this variant impacts protein function (PMID: 18535179) (PS3_supporting).
PM3_Strong
This variant has been detected in at least 12 individuals with autosomal recessive limb-girdle muscular dystrophy. Of those individuals, two were confirmed compound heterozygous for the variant and a pathogenic or likely pathogenic variant (c.850C>T, 2 pts, PMID: 12566530, LOVD). Ten patients were homozygous for the variant (1 pt, PMID: 12566530, 23989969, 7663524, 37628638) (PM3_Strong).
PP1_Strong
The variant has been reported to segregate with autosomal recessive limb girdle muscular dystrophy in 10 affected family members from five families (PP1_Strong; LOVD, PMID: 12566530, 7663524).
Not Met criteria codes
BP5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP7
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PVS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
The filtering allele frequency of this variant is 0.0004392 (the lower threshold of the 95% CI of 62/112872 exome chromosomes) in the European (non-Finnish) population in gnomAD v2.1.1, which is lower than the ClinGen LGMD VCEP threshold (>0.0009) for BS1 (BS1, PM2 not met).
Curation History
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