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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 stars
criteria provided, multiple submitters, no conflicts
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no 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
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

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000030265OMIM
no assertion criteria provided
Pathogenic
(May 1, 2008)
germlineliterature only

PubMed (3)
[See all records that cite these PMIDs]

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.,

SCV000538063Knight Diagnostic Laboratories, Oregon Health and Sciences University - CSER-NextGen
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Jan 27, 2016)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV000649765Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(Jan 27, 2024)
germlineclinical testing

PubMed (13)
[See all records that cite these PMIDs]

SCV000786715Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard - Broad Institute Center for Mendelian Genomics (CMG)
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenicgermlineresearch

PubMed (1)
[See all records that cite this PMID]

SCV000894134Fulgent Genetics, Fulgent Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Oct 6, 2021)
unknownclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV001149922Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München
criteria provided, single submitter

(Classification criteria August 2017)
Pathogenic
(Jan 16, 2020)
germlineclinical testing

Citation Link,

SCV001194172Myriad Genetics, Inc.
criteria provided, single submitter

(Myriad Women's Health Autosomal Recessive and X-Linked Classification Criteria (2019))
Pathogenic
(Nov 12, 2019)
unknownclinical testing

PubMed (4)
[See all records that cite these PMIDs]

Citation Link,

SCV001368150Centre for Mendelian Genomics, University Medical Centre Ljubljana
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Jan 1, 2016)
unknownclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV001453377Natera, Inc.
no assertion criteria provided
Pathogenic
(Sep 16, 2020)
germlineclinical testing

SCV002020093Revvity Omics, Revvity
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(May 17, 2023)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV003931646Genome-Nilou Lab
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Feb 8, 2023)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV004203146Baylor Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Mar 28, 2024)
unknownclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV004847588Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Mar 30, 2022)
germlineclinical testing

PubMed (17)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot provided1not providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlinenonot providednot providednot providednot providednot providedclinical testing
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedunknownyesnot providednot providednot providednot providednot providedclinical testing
Unspecifiedgermlineyes11not providednot providednot providedresearch

Citations

PubMed

Adhalin gene mutations in patients with autosomal recessive childhood onset muscular dystrophy with adhalin deficiency.

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.

PubMed [citation]
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.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818
See all PubMed Citations (20)
PMC

Standards and Guidelines for the Interpretation of Sequence Variants: A Joint Consensus Recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

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

PMC [article]
PMCID:
PMC4544753
PMID:
25741868
DOI:
10.1038/gim.2015.30

Details of each submission

From OMIM, SCV000030265.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature 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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

From Knight Diagnostic Laboratories, Oregon Health and Sciences University - CSER-NextGen, SCV000538063.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical 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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenonot providednot providednot providednot providednot providednot providednot provided

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000649765.10

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical 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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard - Broad Institute Center for Mendelian Genomics (CMG), SCV000786715.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1Unspecified1not providednot providedresearch 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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not provided1not provided

From Fulgent Genetics, Fulgent Genetics, SCV000894134.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München, SCV001149922.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyes1bloodnot provided1not providednot providednot provided

From Myriad Genetics, Inc., SCV001194172.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical 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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Centre for Mendelian Genomics, University Medical Centre Ljubljana, SCV001368150.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This variant was classified as: Pathogenic. This variant was detected in homozygous state.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot providednot providednot providednot providednot provided

From Natera, Inc., SCV001453377.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Revvity Omics, Revvity, SCV002020093.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Genome-Nilou Lab, SCV003931646.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Baylor Genetics, SCV004203146.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV004847588.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical 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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 10, 2024