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.197T>A (p.Leu66His)

CA501057

286025 (ClinVar)

Gene: SGCA (HGNC:6442)
Condition: autosomal recessive limb-girdle muscular dystrophy (MONDO:0015152)
Inheritance Mode: Autosomal recessive inheritance
UUID: 56729249-dce6-49b4-914a-03a511954b23
Approved on: 2026-04-29
Published on: 2026-05-07

HGVS expressions

NM_000023.4(SGCA):c.197T>A (p.Leu66His)
NM_000023.4:c.197T>A
NC_000017.11:g.50167621T>A
CM000679.2:g.50167621T>A
NC_000017.10:g.48244982T>A
CM000679.1:g.48244982T>A
NC_000017.9:g.45599981T>A
NG_008889.1:g.6617T>A
ENST00000504073.2:c.197T>A
ENST00000511303.6:n.38-326T>A
ENST00000512526.2:c.197T>A
ENST00000682109.1:c.77T>A
ENST00000683294.1:c.197T>A
ENST00000262018.8:c.197T>A
ENST00000262018.7:c.197T>A
ENST00000344627.10:c.197T>A
ENST00000502555.5:c.157+134T>A
ENST00000511303.5:c.34-326T>A
ENST00000512526.1:c.41T>A
ENST00000513821.5:c.197T>A
ENST00000513942.5:n.104-326T>A
ENST00000514934.1:c.*18+134T>A
NM_000023.2:c.197T>A
NM_001135697.1:c.197T>A
NM_000023.3:c.197T>A
NM_001135697.2:c.197T>A
NR_135553.1:n.253T>A
NM_001135697.3:c.197T>A
NR_135553.2:n.233T>A
More

Likely Pathogenic

Met criteria codes 4
PS3_Moderate PP3 PM3 PP4_Strong
Not Met criteria codes 2
BS1 PM2

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 2.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Limb Girdle Muscular Dystrophy VCEP
The NM_000023.4: c.197T>A variant in SGCA is a missense variant predicted to cause substitution of leucine by histidine at amino acid 66, p.(Leu66His). This variant has been detected in at least 10 individuals with limb-girdle muscular dystrophy, all of them were homozygous for the variant (1 pt; PMIDs: 33552634, 30564623, 31069529, 35416532) (PM3). At least one patient homozygous for this variant displayed progressive limb girdle muscle weakness and absent alpha-sarcoglycan protein expression, which is highly specific for SGCA-related LGMD (PP4_Strong; PMID: 35416532). The upper bound of the 95% confidence interval of the Grpmax variant allele frequency in gnomAD v4.1.1 is 0.0001724 (9/91072 South Asian alleles), which is higher than the LGMD VCEP threshold (<0.00009) for PM2_Supporting, and therefore does not meet this criterion. An in vitro assay in a heterologous cell system has demonstrated that this variant disrupts membrane localization of the sarcoglycan complex, indicating disruption of protein function (PS3_Moderate, Washington University internal data). The computational predictor REVEL also gives a score of 0.887, 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 2.0.0; 04/29/2026): PM3, PP4_Strong, PS3_Moderate, PP3.
Met criteria codes
PS3_Moderate
An in vitro assay in a heterologous cell system has demonstrated that this variant disrupts membrane localization of the sarcoglycan complex, indicating disruption of protein function (PS3_Moderate, Washington University internal data). score -0.97 (WashU assay), -2.21 (Lek Yale assay)
PP3
The computational predictor REVEL gives a score of 0.887, 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 10 individuals with limb-girdle muscular dystrophy, all of whom were homozygous for the variant (1 pt; PMIDs: 33552634, 30564623, 31069529, 35416532) (PM3).
PP4_Strong
At least one patient homozygous for this variant displayed progressive limb girdle muscle weakness and absent alpha-sarcoglycan protein expression, which is highly specific for SGCA-related LGMD (PP4_Strong; PMID: 35416532).
Not Met criteria codes
BS1
The filtering allele frequency of the variant is 0.000051556 for South Asian alleles in gnomAD v4.1.0 (the lower threshold of the 95% CI of 9/91072), which is lower than the LGMD VCEP threshold (>0.0009) for BS1, and therefore does not meet this criterion.
PM2
The upper bound of the 95% confidence interval of the Grpmax variant allele frequency in gnomAD v4.1.1 is 0.0001724 (9/91072 South Asian alleles), which is higher than the LGMD VCEP threshold (<0.00009) for PM2_Supporting, and therefore does not meet this criterion. This variant seems to be a South Asian founder variant.
Curation History
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