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.101G>A (p.Arg34His)

CA199071

92301 (ClinVar)

Gene: SGCA
Condition: autosomal recessive limb-girdle muscular dystrophy
Inheritance Mode: Autosomal recessive inheritance
UUID: 5fe1934d-e35e-4f18-9095-389cc95f3639
Approved on: 2025-01-09
Published on: 2025-01-30

HGVS expressions

NM_000023.4:c.101G>A
NM_000023.4(SGCA):c.101G>A (p.Arg34His)
NC_000017.11:g.50167431G>A
CM000679.2:g.50167431G>A
NC_000017.10:g.48244792G>A
CM000679.1:g.48244792G>A
NC_000017.9:g.45599791G>A
NG_008889.1:g.6427G>A
ENST00000504073.2:c.101G>A
ENST00000511303.6:n.38-516G>A
ENST00000512526.2:c.101G>A
ENST00000682109.1:c.38-151G>A
ENST00000683294.1:c.101G>A
ENST00000262018.8:c.101G>A
ENST00000262018.7:c.101G>A
ENST00000344627.10:c.101G>A
ENST00000502555.5:c.101G>A
ENST00000511303.5:c.34-516G>A
ENST00000513821.5:c.101G>A
ENST00000513942.5:n.104-516G>A
ENST00000514934.1:c.160G>A
NM_000023.2:c.101G>A
NM_001135697.1:c.101G>A
NM_000023.3:c.101G>A
NM_001135697.2:c.101G>A
NR_135553.1:n.157G>A
NM_001135697.3:c.101G>A
NR_135553.2:n.137G>A
More

Likely Pathogenic

Met criteria codes 4
PM2_Supporting PP3 PM3 PP4_Strong
Not Met criteria codes 1
PM5

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.101G>A variant in SGCA is a missense variant predicted to cause substitution of arginine by histidine at amino acid 34 (p.Arg34His). This variant has been detected in at least two individuals with autosomal recessive limb girdle muscular dystrophy. Of those individuals, one was compound heterozygous for the variant and a pathogenic or likely pathogenic variant (p.Arg77Cys, 1.0 pt, PMID: 18285821) (PM3). At least one patient with this variant and a second presumed diagnostic SGCA variant displayed progressive limb girdle muscle weakness as well as significantly reduced or absent expression of alpha-sarcoglycan protein, which is highly specific for SGCA-related LGMD (PP4_Strong; PMID: 1828582). The filtering allele frequency of this variant is 0.000023 (the upper threshold of the 95% CI of 6/113724 exome chromosomes) in the European (non-Finnish) population in gnomAD v2.1.1, which is lower than the ClinGen LGMD VCEP threshold (0.00009) for PM2_Supporting and therefore meets this criterion (PM2_Supporting). The computational predictor REVEL gives a score of 0.708, 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, PM2_Supporting, PM3, PP3.
Met criteria codes
PM2_Supporting
The filtering allele frequency of this variant is 0.000023 (the upper threshold of the 95% CI of 6/113724 exome chromosomes) in the European (non-Finnish) population in gnomAD v2.1.1, which is lower than the ClinGen LGMD VCEP threshold (0.00009) for PM2_Supporting and therefore meets this criterion (PM2_Supporting).
PP3
The computational predictor REVEL gives a score of 0.708, 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 two individuals with autosomal recessive limb girdle muscular dystrophy. Of those individuals, one was compound heterozygous for the variant and a pathogenic or likely pathogenic variant (p.Arg77Cys, 1.0 pt, PMID: 18285821) (PM3).
PP4_Strong
At least one patient with this variant and a second SGCA variant displayed progressive limb girdle muscle weakness as well as significantly reduced or absent expression of alpha-sarcoglycan protein, which is highly specific for SGCA-related LGMD (PP4_Strong; PMID: 1828582).
Not Met criteria codes
PM5
Cannot use PM5 as this variant was used to apply PM5 to p.Arg34Cys.
Curation History
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