NM_000023.4(SGCA):c.229C>T (p.Arg77Cys) AND Autosomal recessive limb-girdle muscular dystrophy type 2D
- Germline classification:
- Pathogenic (13 submissions)
- Last evaluated:
- Mar 28, 2024
- Review status:
- 2 stars out of maximum of 4 starscriteria provided, multiple submitters, no conflicts
- Somatic classification
of clinical impact: - None
- Review status:
- (0/4) 0 stars out of maximum of 4 starsno assertion criteria provided
- Somatic classification
of oncogenicity: - None
- Review status:
- (0/4) 0 stars out of maximum of 4 starsno assertion criteria provided
- Record status:
- current
- Accession:
- RCV000010044.51
Allele description [Variation Report for NM_000023.4(SGCA):c.229C>T (p.Arg77Cys)]
NM_000023.4(SGCA):c.229C>T (p.Arg77Cys)
- Gene:
- SGCA:sarcoglycan alpha [Gene - OMIM - HGNC]
- Variant type:
- single nucleotide variant
- Cytogenetic location:
- 17q21.33
- Genomic location:
- Preferred name:
- NM_000023.4(SGCA):c.229C>T (p.Arg77Cys)
- HGVS:
- NC_000017.11:g.50167653C>T
- NG_008889.1:g.6649C>T
- NM_000023.4:c.229C>TMANE SELECT
- NM_001135697.3:c.229C>T
- NP_000014.1:p.Arg77Cys
- NP_000014.1:p.Arg77Cys
- NP_001129169.1:p.Arg77Cys
- LRG_203t1:c.229C>T
- LRG_203:g.6649C>T
- LRG_203p1:p.Arg77Cys
- NC_000017.10:g.48245014C>T
- NM_000023.2:c.229C>T
- NM_000023.3:c.229C>T
- NR_135553.2:n.265C>T
- Q16586:p.Arg77Cys
This HGVS expression did not pass validation- Protein change:
- R77C; ARG77CYS
- Links:
- UniProtKB: Q16586#VAR_010387; OMIM: 600119.0003; dbSNP: rs28933693
- NCBI 1000 Genomes Browser:
- rs28933693
- Molecular consequence:
- NM_000023.4:c.229C>T - missense variant - [Sequence Ontology: SO:0001583]
- NM_001135697.3:c.229C>T - missense variant - [Sequence Ontology: SO:0001583]
- NR_135553.2:n.265C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
- Observations:
- 1
Condition(s)
- Name:
- Autosomal recessive limb-girdle muscular dystrophy type 2D (LGMDR3)
- Synonyms:
- ADHALINOPATHY, PRIMARY; Limb-girdle muscular dystrophy, type 2D; Muscular dystrophy limb-girdle with alpha-sarcoglycan; See all synonyms [MedGen]
- Identifiers:
- MONDO: MONDO:0011968; MedGen: C2936332; Orphanet: 62; OMIM: 608099
-
Abnormality of the hand
Abnormality of the handMedGen
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See more...Assertion and evidence details
Submission Accession | Submitter | Review Status (Assertion method) | Clinical Significance (Last evaluated) | Origin | Method | Citations |
---|---|---|---|---|---|---|
SCV000030265 | OMIM | no assertion criteria provided | Pathogenic (May 1, 2008) | germline | literature only | PubMed (3) Piccolo, F., Roberds, S. L., Jeanpierre, M., Leturcq, F., Azibi, K., Beldjord, C., Carrie, A., Recan, D., Chaouch, M., Reghis, A., El Kerch, F., Sefiani, A., Voit, T., Merlini, L., Collin, H., Eymard, B., Beckmann, J. S., Romero, N. B., Tome, F. M. S., Fardeau, M., Campbell, K. P., Kaplan, J.-C. Primary adhalinopathy: a common cause of autosomal recessive muscular dystrophy of variable severity. Nature Genet. 10: 243-245, 1995. Note: Erratum: Nature Genet. 11: 104 only, 1995., |
SCV000538063 | Knight Diagnostic Laboratories, Oregon Health and Sciences University - CSER-NextGen | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Jan 27, 2016) | germline | clinical testing | |
SCV000649765 | Labcorp Genetics (formerly Invitae), Labcorp | criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) | Pathogenic (Jan 27, 2024) | germline | clinical testing | |
SCV000786715 | Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard - Broad Institute Center for Mendelian Genomics (CMG) | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic | germline | research | |
SCV000894134 | Fulgent Genetics, Fulgent Genetics | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Oct 6, 2021) | unknown | clinical testing | |
SCV001149922 | Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München | criteria provided, single submitter (Classification criteria August 2017) | Pathogenic (Jan 16, 2020) | germline | clinical testing | |
SCV001194172 | Myriad Genetics, Inc. | criteria provided, single submitter (Myriad Women's Health Autosomal Recessive and X-Linked Classification Criteria (2019)) | Pathogenic (Nov 12, 2019) | unknown | clinical testing | |
SCV001368150 | Centre for Mendelian Genomics, University Medical Centre Ljubljana | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Jan 1, 2016) | unknown | clinical testing | |
SCV001453377 | Natera, Inc. | no assertion criteria provided | Pathogenic (Sep 16, 2020) | germline | clinical testing | |
SCV002020093 | Revvity Omics, Revvity | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (May 17, 2023) | germline | clinical testing | |
SCV003931646 | Genome-Nilou Lab | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Feb 8, 2023) | germline | clinical testing | |
SCV004203146 | Baylor Genetics | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Mar 28, 2024) | unknown | clinical testing | |
SCV004847588 | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Mar 30, 2022) | germline | clinical testing |
Summary from all submissions
Ethnicity | Origin | Affected | Individuals | Families | Chromosomes tested | Number Tested | Family history | Method |
---|---|---|---|---|---|---|---|---|
not provided | germline | yes | 1 | not provided | not provided | 1 | not provided | clinical testing |
not provided | germline | unknown | not provided | not provided | not provided | not provided | not provided | clinical testing |
not provided | unknown | unknown | not provided | not provided | not provided | not provided | not provided | clinical testing |
not provided | germline | no | not provided | not provided | not provided | not provided | not provided | clinical testing |
not provided | germline | not provided | not provided | not provided | not provided | not provided | not provided | literature only |
not provided | unknown | yes | not provided | not provided | not provided | not provided | not provided | clinical testing |
Unspecified | germline | yes | 1 | 1 | not provided | not provided | not provided | research |
Citations
PubMed
Kawai H, Akaike M, Endo T, Adachi K, Inui T, Mitsui T, Kashiwagi S, Fujiwara T, Okuno S, Shin S, et al.
J Clin Invest. 1995 Sep;96(3):1202-7.
- PMID:
- 7657792
- PMCID:
- PMC185739
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.
Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.
Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.
- PMID:
- 28492532
- PMCID:
- PMC5632818
PMC
Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL.
Genetics in medicine : official journal of the American College of Medical Genetics. 2015 Mar 5; 17(5): 405-424
- PMCID:
- PMC4544753
- PMID:
- 25741868
- DOI:
- 10.1038/gim.2015.30
Details of each submission
From OMIM, SCV000030265.3
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | literature only | PubMed (3) |
Description
In a German family with Duchenne-like muscular dystrophy of intermediate severity (LGMDR3; 608099), Piccolo et al. (1995) found a homozygous CGC-to-TGC transition in exon 3 of the SGCA gene, resulting in an arg77-to-cys (R77C) substitution. The same mutation was found in the heterozygous state in 2 apparently unrelated French families in which the affected individuals were compound heterozygotes. In a note added in proof, Piccolo et al. (1995) commented that out of a total of 46 mutated chromosomes from unrelated families in Europe and the US, 11 had the R77C mutation. Four patients were homozygous for the mutation.
Passos Bueno et al. (1995) identified the same mutation in 3 Brazilian families with a relatively mild form of LGMD2D.
In a Japanese patient with autosomal recessive childhood-onset muscular dystrophy from a consanguineous family, Kawai et al. (1995) found homozygosity for the R77C mutation. Muscle biopsy showed complete absence of adhalin.
Bartoli et al. (2008) found that SGCA with the R77C mutation was retained in the endoplasmic reticulum (ER), where it formed aggregates. Surface expression of mutant SGCA could be rescued by inhibiting its degradation via proteasome-mediated ER-associated degradation (ERAD) or by inhibiting mannosidase I (MAN1B1; 604346), an ER enzyme that directs misfolded glycoproteins toward ERAD.
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | not provided | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Knight Diagnostic Laboratories, Oregon Health and Sciences University - CSER-NextGen, SCV000538063.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
Description
The c.229C>T (p.Arg77Cys) missense variant in the SGCA gene is the most common pathogenic variant reported in individuals affected with autosomal recessive Limb-girdle muscular dystrophy, type 2D (Piccolo et al., 1995; Carrié et al., 1997; Hackman et al., 2005). This variant is located within a mutational hotspot with variants in exon 3 accounting for up to 46% of the affected alleles (Carrié et al., 1997). This variant has been shown to co-segregate with disease in multiple families (Bueno et al., 1995; Kawai et al., 1995). Functional studies have shown this variant results in improper localization of the protein with its retention in the ER as opposed to the plasma membrane (Bartoli et al., 2008). The c.229C>T variant has been reported at low frequency in the control population databases (Exome Sequencing Project [ESP] = 0.081%, 1000 Genomes = 0.3%, and ExAC = 0.154%). Multiple in silico algorithms predict this variant to have a deleterious effect (GERP = 4.53; CADD = 26.5; PolyPhen = 1; SIFT = 0), and multiple reputable diagnostic laboratories report this variant as pathogenic. Therefore, this collective evidence supports the classification of the c.229C>T (p.Arg77Cys) as a recessive Pathogenic variant for Limb-girdle muscular dystrophy, type 2D.
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | no | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Labcorp Genetics (formerly Invitae), Labcorp, SCV000649765.10
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (13) |
Description
This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 77 of the SGCA protein (p.Arg77Cys). This variant is present in population databases (rs28933693, gnomAD 0.2%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individual(s) with limb girdle muscular dystrophy type 2D (PMID: 7663524, 9032047, 9153448, 9192266, 15298081, 18285821, 18421900, 21856579, 25135358). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 9437). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on SGCA protein function. Experimental studies have shown that this missense change affects SGCA function (PMID: 16787395, 18252745, 22095924). For these reasons, this variant has been classified as Pathogenic.
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard - Broad Institute Center for Mendelian Genomics (CMG), SCV000786715.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | Unspecified | 1 | not provided | not provided | research | PubMed (1) |
Description
The homozgous p.Arg77Cys variant was identified by our study in one individual with Limb-Girdle Muscular Dystrophy. The p.Arg77Cys variant is believed to be pathogenic based on numberous reports by other laboratories in the literature and databases.
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | yes | not provided | not provided | not provided | 1 | not provided | 1 | not provided |
From Fulgent Genetics, Fulgent Genetics, SCV000894134.2
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | unknown | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München, SCV001149922.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | 1 | not provided | not provided | clinical testing | not provided |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | yes | 1 | blood | not provided | 1 | not provided | not provided | not provided |
From Myriad Genetics, Inc., SCV001194172.2
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (4) |
Description
NM_000023.2(SGCA):c.229C>T(R77C) is classified as pathogenic in the context of alpha-sarcoglycanopathy. Sources cited for classification include the following: PMID 15736300, 18252745, 9192266 and 18996010. Classification of NM_000023.2(SGCA):c.229C>T(R77C) is based on the following criteria: This is a well-established pathogenic variant in the literature that has been observed more frequently in patients with clinical diagnoses than in healthy populations. Please note: this variant was assessed in the context of healthy population screening.
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | unknown | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Centre for Mendelian Genomics, University Medical Centre Ljubljana, SCV001368150.2
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
Description
This variant was classified as: Pathogenic. This variant was detected in homozygous state.
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | unknown | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Natera, Inc., SCV001453377.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | not provided |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Revvity Omics, Revvity, SCV002020093.3
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Genome-Nilou Lab, SCV003931646.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Baylor Genetics, SCV004203146.2
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | unknown | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV004847588.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (17) |
Description
The p.Arg77Cys variant in SGCA is the most common pathogenic variant in limb girdle muscular dystrophy type 2D (LGMD2D) having been reported in >20 homozygous or compound heterozygous individuals with LGMD2D and segregating in at least 4 affected family members (Bueno 1995 PMID: 8528203, Carrie 1997 PMID: 9192266, Boito 2005 PMID: 12746421, Hackman 2005 PMID: 15736300, Tetreault 2011 PMID: 21856579, Fayssoil 2016 PMID: 21856579, Avila De Salman 2007 PMID: 18421900, Walter 2004 PMID: 15298081, Stehlíková 2014 PMID: 25135358, Trabelsi 2008 PMID: 18285821, Duggan 1997 PMID: 9032047, Piccolo 1995 PMID: 7663524, Eymard 1997 PMID: 9153448). This variant has also been reported in ClinVar (Variation ID 9437) and has been identified in 0.18% (47/24978) of Finnish chromosomes and in 0.05% (69/128290) of European chromosomes by gnomAD (http://gnomAD.broadinstitute.org). Computational prediction tools and conservation analyses suggest that this variant may impact the protein. In vitro functional studies provide some evidence that this variant impacts protein function by trapping the protein in the endoplasmic reticulum where it is ultimately degraded (Bartoli 2008 PMID: 18252745, Soheili 2012 PMID: 22095924, Gastaldello 2008 PMID: 18535179, Draviam 2006 PMID: 16787395). In summary, this variant meets criteria to be classified as pathogenic for autosomal recessive limb girdle muscular dystrophy type 2D. ACMG/AMP criteria applied: PM3_VeryStrong, PS3_Moderate, PP1_Moderate, PP3.
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
Last Updated: Nov 10, 2024