SGCB

sarcoglycan beta

Basic information

Region (hg38): 4:52020706-52038299

Previous symbols: [ "LGMD2E" ]

Links

ENSG00000163069 ∙ NCBI:6443 ∙ OMIM:600900 ∙ HGNC:10806 ∙ Uniprot:Q16585 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• autosomal recessive limb-girdle muscular dystrophy type 2E (Definitive), mode of inheritance: AR
• autosomal recessive limb-girdle muscular dystrophy type 2E (Definitive), mode of inheritance: AR
• autosomal recessive limb-girdle muscular dystrophy type 2E (Supportive), mode of inheritance: AR
• autosomal recessive limb-girdle muscular dystrophy type 2E (Strong), mode of inheritance: AR
• autosomal recessive limb-girdle muscular dystrophy (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Muscular dystrophy, limb-girdle, autosomal recessive, 4	AR	Cardiovascular	The condition can include severe cardiac manifestations, including lethal ventricular arrhythmias and dilated cardiomyopathy and knowledge may allow surveillance (eg, with EKG, echocardiogram, and Holter monitoring) and early medical management, which may ameliorate morbidity and mortality; Heart transplantation may be indicated in individuals with severe dilated cardiomyopathy	Cardiovascular; Musculoskeletal	7581448; 8968749; 7581449; 18285821; 20627570
Digenic inheritance (with SGCD) has been suggested, but the evidence is unclear

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SGCB gene.

• Autosomal recessive limb-girdle muscular dystrophy type 2E (36 variants)
• not provided (5 variants)
• Abnormality of the musculature (1 variants)
• Autosomal recessive limb-girdle muscular dystrophy (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SGCB gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			2	119		121
missense		9	124			133
nonsense	4	9				13
start loss	3	4				7
frameshift	27	27	3			57
inframe indel			6			6
splice donor/acceptor (+/-2bp)	4	10	1			15
splice region			7	11	1	19
non coding			60	69	12	141
Total	38	59	196	188	12

Highest pathogenic variant AF is 0.00000662

Variants in SGCB

This is a list of pathogenic ClinVar variants found in the SGCB region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
4-52020741-T-C		Limb-girdle muscular dystrophy, recessive • Qualitative or quantitative defects of beta-sarcoglycan	Uncertain significance (Jan 12, 2018)
4-52020744-C-A		Qualitative or quantitative defects of beta-sarcoglycan	Uncertain significance (Jan 12, 2018)
4-52020821-A-G		Qualitative or quantitative defects of beta-sarcoglycan	Uncertain significance (Jan 12, 2018)
4-52020901-A-C		Qualitative or quantitative defects of beta-sarcoglycan	Uncertain significance (Jan 12, 2018)
4-52020914-T-C		Qualitative or quantitative defects of beta-sarcoglycan	Likely benign (Jan 13, 2018)
4-52020973-C-T		Limb-girdle muscular dystrophy, recessive • Qualitative or quantitative defects of beta-sarcoglycan	Uncertain significance (Jan 12, 2018)
4-52020987-T-C		Qualitative or quantitative defects of beta-sarcoglycan	Uncertain significance (Jan 12, 2018)
4-52020996-ATTTAT-A		Limb-girdle muscular dystrophy, recessive • Qualitative or quantitative defects of beta-sarcoglycan	Uncertain significance (Jun 14, 2016)
4-52021050-A-G		Limb-girdle muscular dystrophy, recessive • Qualitative or quantitative defects of beta-sarcoglycan	Conflicting classifications of pathogenicity (Feb 01, 2023)
4-52021143-T-C		Qualitative or quantitative defects of beta-sarcoglycan	Uncertain significance (Jan 12, 2018)
4-52021146-C-T		Limb-girdle muscular dystrophy, recessive • Qualitative or quantitative defects of beta-sarcoglycan	Uncertain significance (Jan 13, 2018)
4-52021193-C-T		Qualitative or quantitative defects of beta-sarcoglycan • Limb-girdle muscular dystrophy, recessive	Uncertain significance (Jan 13, 2018)
4-52021250-A-G		Limb-girdle muscular dystrophy, recessive • Qualitative or quantitative defects of beta-sarcoglycan	Uncertain significance (Jan 12, 2018)
4-52021377-G-A		Qualitative or quantitative defects of beta-sarcoglycan • Limb-girdle muscular dystrophy, recessive	Uncertain significance (Jan 13, 2018)
4-52021463-C-A		Qualitative or quantitative defects of beta-sarcoglycan	Uncertain significance (Jan 13, 2018)
4-52021513-C-T		Qualitative or quantitative defects of beta-sarcoglycan	Uncertain significance (Jan 13, 2018)
4-52021534-G-C		Qualitative or quantitative defects of beta-sarcoglycan	Uncertain significance (Jan 13, 2018)
4-52021570-T-A		Qualitative or quantitative defects of beta-sarcoglycan	Uncertain significance (Jan 12, 2018)
4-52021606-G-A		Limb-girdle muscular dystrophy, recessive • Qualitative or quantitative defects of beta-sarcoglycan	Uncertain significance (Jan 12, 2018)
4-52021671-A-T		Limb-girdle muscular dystrophy, recessive • Qualitative or quantitative defects of beta-sarcoglycan	Conflicting classifications of pathogenicity (Jan 13, 2018)
4-52021675-T-A		Qualitative or quantitative defects of beta-sarcoglycan	Likely benign (Mar 06, 2018)
4-52021791-A-G		Limb-girdle muscular dystrophy, recessive • Qualitative or quantitative defects of beta-sarcoglycan	Uncertain significance (Jan 12, 2018)
4-52021810-G-A		Qualitative or quantitative defects of beta-sarcoglycan	Uncertain significance (Jan 12, 2018)
4-52021827-TA-T		Limb-girdle muscular dystrophy, recessive • Qualitative or quantitative defects of beta-sarcoglycan	Uncertain significance (Jun 14, 2016)
4-52021860-A-C		Limb-girdle muscular dystrophy, recessive • Qualitative or quantitative defects of beta-sarcoglycan	Benign (Jan 12, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SGCB	protein_coding	protein_coding	ENST00000381431	6	17777

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.58e-7	0.334	125725	0	23	125748	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.00497	178	178	1.00	0.00000939	2130
Missense in Polyphen		43	51.808	0.82999		571
Synonymous	-0.978	68	58.5	1.16	0.00000289	588
Loss of Function	0.415	10	11.5	0.868	6.34e-7	150

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000905	0.0000904
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000217	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000114	0.000114
Middle Eastern	0.000217	0.000217
South Asian	0.0000982	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the sarcoglycan complex, a subcomplex of the dystrophin-glycoprotein complex which forms a link between the F-actin cytoskeleton and the extracellular matrix.
• Disease: DISEASE: Limb-girdle muscular dystrophy 2E (LGMD2E) [MIM:604286]: An autosomal recessive degenerative myopathy characterized by pelvic and shoulder muscle wasting, onset usually in childhood and variable progression rate. {ECO:0000269|PubMed:8968749, ECO:0000269|PubMed:9032047, ECO:0000269|PubMed:9565988, ECO:0000269|PubMed:9631401}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Dilated cardiomyopathy (DCM) - Homo sapiens (human);Viral myocarditis - Homo sapiens (human);Arrhythmogenic right ventricular cardiomyopathy (ARVC) - Homo sapiens (human);Hypertrophic cardiomyopathy (HCM) - Homo sapiens (human);Arrhythmogenic Right Ventricular Cardiomyopathy (Consensus)

Recessive Scores

• pRec: 0.116

Intolerance Scores

• loftool: 0.188
• rvis_EVS: -0.23
• rvis_percentile_EVS: 37.11

Haploinsufficiency Scores

• pHI: 0.200
• hipred: N
• hipred_score: 0.385
• ghis: 0.576

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.112

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Sgcb
• Phenotype: growth/size/body region phenotype; muscle phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); immune system phenotype

Gene ontology

• Biological process: muscle organ development;muscle fiber development;cardiac muscle cell development;vascular smooth muscle cell development
• Cellular component: cytoplasm;cytoskeleton;integral component of plasma membrane;dystrophin-associated glycoprotein complex;sarcoglycan complex;sarcolemma