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    SGCD sarcoglycan delta [ Homo sapiens (human) ]

    Gene ID: 6444, updated on 10-Dec-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: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 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
    		Compare labs
    Limb-girdle muscular dystrophy
    MedGen: C0686353 GeneReviews: Not available
    		Compare labs
    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)

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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