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.850C>T (p.Arg284Cys)

CA120431

9439 (ClinVar)

Gene: SGCA
Condition: autosomal recessive limb-girdle muscular dystrophy
Inheritance Mode: Autosomal recessive inheritance
UUID: 2be0d4bd-6c77-428b-b4c4-bade2036ef27
Approved on: 2025-01-09
Published on: 2025-01-09

HGVS expressions

NM_000023.4:c.850C>T
NM_000023.4(SGCA):c.850C>T (p.Arg284Cys)
NC_000017.11:g.50170245C>T
CM000679.2:g.50170245C>T
NC_000017.10:g.48247606C>T
CM000679.1:g.48247606C>T
NC_000017.9:g.45602605C>T
NG_008889.1:g.9241C>T
ENST00000504073.2:c.700C>T
ENST00000511303.6:n.310-395C>T
ENST00000512526.2:c.576-395C>T
ENST00000682109.1:c.730C>T
ENST00000683226.1:n.1448C>T
ENST00000683294.1:c.*59+57C>T
ENST00000683544.1:n.216C>T
ENST00000262018.8:c.850C>T
ENST00000262018.7:c.850C>T
ENST00000344627.10:c.585-395C>T
ENST00000504073.1:c.167C>T
ENST00000511303.5:c.306-395C>T
ENST00000512526.1:c.420-395C>T
ENST00000513821.5:c.748-395C>T
ENST00000513942.5:n.376-395C>T
NM_000023.2:c.850C>T
NM_001135697.1:c.585-395C>T
NM_000023.3:c.850C>T
NM_001135697.2:c.585-395C>T
NR_135553.1:n.804-395C>T
NM_001135697.3:c.585-395C>T
NR_135553.2:n.784-395C>T
More

Pathogenic

Met criteria codes 4
PP4_Strong PM3_Strong PP1 PP3
Not Met criteria codes 2
PM2 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.850C>T variant in SGCA is a missense variant predicted to cause substitution of arginine by cysteine at amino acid 284 (p.Arg284Cys). This variant has been detected in at least five 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 (c.241C>T p.(Arg81Cys), 1 pt, PMID: 17994539), and two were homozygous for the variant (1 pt, PMID: 26404900, 26453141) (PM3_Strong). At least one patient with this variant and a second presumed diagnostic variant in SGCA 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; UCSD internal clinic data communication, PMID: 17994539). 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 minor allele frequency for this variant is 0.0002205 in the European (non-Finnish) population of gnomAD v3.1.2 (15/68028 genome chromosomes), which exceeds the LGMD VCEP threshold of 0.00009 for PM2_Supporting (criterion not met). The computational predictor REVEL gives a score of 0.754, 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 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_Strong, PP1, PP3.
Met criteria codes
PP4_Strong
At least one patient with this 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; internal clinic data, PMID: 17994539). GRASP patient had panel test
PM3_Strong
This variant has been detected in at least five 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 (c.241C>T p.(Arg81Cys),1 pt, PMID: 17994539), and two were homozygous for the variant (1 pt, PMID: 26404900, 26453141) (PM3_Strong).
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 0.754, which is above the threshold of 0.7, evidence that correlates with impact to SGCA function (PP3).
Not Met criteria codes
PM2
The minor allele frequency for this variant is 0.0002205 in the European (non-Finnish) population of gnomAD v3.1.2 (15/68028 genome chromosomes), which exceeds the LGMD VCEP threshold of 0.00009 for PM2_Supporting (criterion not met).
PM5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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