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SGCD sarcoglycan delta [ Homo sapiens (human) ]

Gene ID: 6444, updated on 2-Nov-2024

Summary

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Official Symbol
SGCDprovided by HGNC
Official Full Name
sarcoglycan deltaprovided by HGNC
Primary source
HGNC:HGNC:10807
See related
Ensembl:ENSG00000170624 MIM:601411; AllianceGenome:HGNC:10807
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SGD; DAGD; 35DAG; CMD1L; SGCDP; LGMDR6; SG-delta
Summary
The protein encoded by this gene is one of the four known components of the sarcoglycan complex, which is a subcomplex of the dystrophin-glycoprotein complex (DGC). DGC forms a link between the F-actin cytoskeleton and the extracellular matrix. This protein is expressed most abundantly in skeletal and cardiac muscle. Mutations in this gene have been associated with autosomal recessive limb-girdle muscular dystrophy and dilated cardiomyopathy. Alternatively spliced transcript variants encoding distinct isoforms have been observed for this gene. [provided by RefSeq, Jul 2008]
Expression
Broad expression in heart (RPKM 13.1), thyroid (RPKM 9.5) and 17 other tissues See more
Orthologs
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Genomic context

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See SGCD in Genome Data Viewer
Location:
5q33.2-q33.3
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (155727832..156767788)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (156261684..157286763)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (155754174..156194799)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene STN1, CST complex subunit pseudogene Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:154854779-154855390 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr5:154963756-154964955 Neighboring gene peptidylprolyl isomerase G pseudogene 1 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr5:155010119-155011318 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:155063444-155063944 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23492 Neighboring gene RNA, 5S ribosomal pseudogene 199 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:155469700-155470248 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:155517127-155518326 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:155628879-155629041 Neighboring gene MPRA-validated peak5548 silencer Neighboring gene uncharacterized LOC124901120 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23493 Neighboring gene NANOG hESC enhancer GRCh37_chr5:155837480-155837981 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:156082668-156083197 Neighboring gene uncharacterized LOC105377673 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23494 Neighboring gene NANOG hESC enhancer GRCh37_chr5:156225176-156225677 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:156229076-156229967 Neighboring gene RNA, U6 small nuclear 556, pseudogene Neighboring gene PPP1R2 family member B

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Linkage analysis in autosomal recessive limb-girdle muscular dystrophy (AR LGMD) maps a sixth form to 5q33-34 (LGMD2F) and indicates that there is at least one more subtype of AR LGMD. Passos-Bueno MR, et al. Hum Mol Genet, 1996 Jun. PMID 8776597
  2. Does delta-sarcoglycan-associated autosomal-dominant cardiomyopathy exist? Bauer R, et al. Eur J Hum Genet, 2009 Sep. PMID 19259135, Free PMC Article
  3. Delta-sarcoglycan gene polymorphism frequency in Amerindian and Mestizo populations of Mexico. Ordoñez-Razo RM, et al. Genet Test Mol Biomarkers, 2010 Apr. PMID 20384457
  4. Impact of delta-sarcoglycan gene polymorphism on the occurrence of coronary spastic angina in Japanese patients with hypertrophic cardiomyopathy. Honda T, et al. Circ J, 2007 Aug. PMID 17652892
  5. Mutations in the delta-sarcoglycan gene are a rare cause of autosomal recessive limb-girdle muscular dystrophy (LGMD2). Duggan DJ, et al. Neurogenetics, 1997 May. PMID 10735275

See all (60) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Study identified 2 non-synonymous missense mutations: c.C652T, p.R218W in ACVRL1, c.C717G, p.D239E in SGCD in Chinese population with total anomalous pulmonary venous return.
    Title: Whole-exome sequencing identifies SGCD and ACVRL1 mutations associated with total anomalous pulmonary venous return (TAPVR) in Chinese population.
  2. Dilated cardiomyopathy mutations in delta-sarcoglycan can exert a dominant negative effect on dystrophin-glycoprotein complex function leading to myocardial mechanical instability that may underlie the pathogenesis of delta-sarcoglycan-associated DCM.
    Title: Dilated cardiomyopathy mutations in δ-sarcoglycan exert a dominant-negative effect on cardiac myocyte mechanical stability.
  3. haplotype -_G composed of c.-100~-110 and A848G confers higher susceptibility to dilated cardiomyopathy in the Mongoloid population.
    Title: A Haplotype of Two Novel Polymorphisms in δ-Sarcoglycan Gene Increases Risk of Dilated Cardiomyopathy in Mongoloid Population.
  4. CC genotype of the delta-sarcoglycan gene polymorphism rs13170573 is associated with obstructive sleep apnea in the Chinese population
    Title: The CC genotype of the delta-sarcoglycan gene polymorphism rs13170573 is associated with obstructive sleep apnea in the Chinese population.
  5. Genetic variation at the delta-sarcoglycan locus elevates heritable sympathetic nerve activity in human twin pairs
    Title: Genetic variation at the delta-sarcoglycan (SGCD) locus elevates heritable sympathetic nerve activity in human twin pairs.
  6. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
    Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
  7. Observational study of genetic testing. (HuGE Navigator)
    Title: A novel custom resequencing array for dilated cardiomyopathy.
  8. Observational study of genotype prevalence. (HuGE Navigator)
    Title: Delta-sarcoglycan gene polymorphism frequency in Amerindian and Mestizo populations of Mexico.
  9. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  10. Observational study and genome-wide association study of gene-disease association and gene-gene interaction. (HuGE Navigator)
    Title: Detecting Genes and Gene-gene Interactions for Age-related Macular Degeneration with a Forest-based Approach.
Submit: New GeneRIF Correction See all GeneRIFs (16)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Autosomal recessive limb-girdle muscular dystrophy type 2F
MedGen: C1832525 OMIM: 601287 GeneReviews: Not available
Compare labs
Dilated cardiomyopathy 1L
MedGen: C1847667 OMIM: 606685 GeneReviews: Not available
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Limb-girdle muscular dystrophy
MedGen: C0686353 GeneReviews: Not available
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Primary dilated cardiomyopathy
MedGen: C0007193 GeneReviews: Dilated Cardiomyopathy Overview
Compare labs

EBI GWAS Catalog

Description
Gene network analysis in a pediatric cohort identifies novel lung function genes.
EBI GWAS Catalog
Genome-wide association analysis of susceptibility and clinical phenotype in multiple sclerosis.
EBI GWAS Catalog
Genome-wide association study of anthropometric traits in Korcula Island, Croatia.
EBI GWAS Catalog
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC22567

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in calcium ion homeostasis IEA
Inferred from Electronic Annotation
more info
  
involved_in calcium-mediated signaling IEA
Inferred from Electronic Annotation
more info
  
involved_in cardiac muscle cell contraction IEA
Inferred from Electronic Annotation
more info
  
involved_in cardiac muscle cell development IEA
Inferred from Electronic Annotation
more info
  
involved_in cardiac muscle tissue development IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in coronary vasculature morphogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in heart contraction IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in muscle organ development TAS
Traceable Author Statement
more info
 PubMed 
involved_in protein-containing complex localization IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in cytoskeleton IEA
Inferred from Electronic Annotation
more info
  
part_of dystrophin-associated glycoprotein complex IDA
Inferred from Direct Assay
more info
 PubMed 
located_in plasma membrane TAS
Traceable Author Statement
more info
 PubMed 
part_of sarcoglycan complex IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in sarcolemma IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in sarcoplasmic reticulum IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
delta-sarcoglycan
Names
35 kDa dystrophin-associated glycoprotein
delta-SG
dystrophin associated glycoprotein, delta sarcoglycan
placental delta sarcoglycan
sarcoglycan, delta (35kDa dystrophin-associated glycoprotein)

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_008693.2 RefSeqGene

    Range
    461414..902446
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_205

mRNA and Protein(s)

  1. NM_000337.6 → NP_000328.2  delta-sarcoglycan isoform 1

    See identical proteins and their annotated locations for NP_000328.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1, also known as SGCD1), encodes the longest isoform (1).
    Source sequence(s)
    AC025434, BC020740, BQ434817, BQ446019, BX537948
    Consensus CDS
    CCDS47325.1
    UniProtKB/Swiss-Prot
    Q92629
    Related
    ENSP00000338343.4, ENST00000337851.9
    Conserved Domains (1) summary
    pfam04790
    Location:24 → 278
    Sarcoglycan_1; Sarcoglycan complex subunit protein

  2. NM_001128209.2 → NP_001121681.1  delta-sarcoglycan isoform 3

    See identical proteins and their annotated locations for NP_001121681.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) is lacking an internal exon from the 5' end compared to transcript variant 1, resulting in translation initiation from the second in-frame AUG, and an isoform (3) missing 1 aa at the N-terminus compared to isoform 1.
    Source sequence(s)
    AC025434, BC020740, BQ434817, BQ446019, BX537948, DA561069
    Consensus CDS
    CCDS47327.1
    UniProtKB/Swiss-Prot
    A8K9S9, Q53XA5, Q92629, Q99644
    Related
    ENSP00000403003.2, ENST00000435422.7
    Conserved Domains (1) summary
    pfam04790
    Location:23 → 277
    Sarcoglycan_1; Sarcoglycan complex subunit protein

  3. NM_172244.3 → NP_758447.1  delta-sarcoglycan isoform 2

    See identical proteins and their annotated locations for NP_758447.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2, also known as SGCD2), contains an alternate 3' terminal exon compared to transcript variant 1. This results in a shorter isoform (2) with a distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AI139498, BQ434817, U58331
    Consensus CDS
    CCDS47326.1
    UniProtKB/Swiss-Prot
    Q92629
    Related
    ENSP00000429378.1, ENST00000517913.5
    Conserved Domains (1) summary
    pfam04790
    Location:29 → 235
    Sarcoglycan_1; Sarcoglycan complex subunit protein

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    155727832..156767788
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047417519.1 → XP_047273475.1  delta-sarcoglycan isoform X1

  2. XM_047417518.1 → XP_047273474.1  delta-sarcoglycan isoform X1

  3. XM_017009724.2 → XP_016865213.1  delta-sarcoglycan isoform X1

    UniProtKB/Swiss-Prot
    Q92629
    Conserved Domains (1) summary
    pfam04790
    Location:24 → 278
    Sarcoglycan_1; Sarcoglycan complex subunit protein

  4. XM_047417520.1 → XP_047273476.1  delta-sarcoglycan isoform X2

    UniProtKB/Swiss-Prot
    A8K9S9, Q53XA5, Q92629, Q99644

  5. XM_005265967.3 → XP_005266024.1  delta-sarcoglycan isoform X3

    Conserved Domains (1) summary
    pfam04790
    Location:29 → 166
    Sarcoglycan_1; Sarcoglycan complex subunit protein

  6. XM_005265966.6 → XP_005266023.1  delta-sarcoglycan isoform X1

    See identical proteins and their annotated locations for XP_005266023.1

    UniProtKB/Swiss-Prot
    Q92629
    Conserved Domains (1) summary
    pfam04790
    Location:24 → 278
    Sarcoglycan_1; Sarcoglycan complex subunit protein

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    156261684..157286763
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054353130.1 → XP_054209105.1  delta-sarcoglycan isoform X1

  2. XM_054353129.1 → XP_054209104.1  delta-sarcoglycan isoform X1

  3. XM_054353128.1 → XP_054209103.1  delta-sarcoglycan isoform X1

  4. XM_054353131.1 → XP_054209106.1  delta-sarcoglycan isoform X2

    UniProtKB/Swiss-Prot
    A8K9S9, Q53XA5, Q92629, Q99644

  5. XM_054353132.1 → XP_054209107.1  delta-sarcoglycan isoform X3

  6. XM_054353127.1 → XP_054209102.1  delta-sarcoglycan isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q92629.2 GenPept UniProtKB/Swiss-Prot:Q92629

Gene LinkOut

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