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    SGCD sarcoglycan delta [ Homo sapiens (human) ]

    Gene ID: 6444, updated on 29-Sep-2018

    Summary

    Official Symbol
    SGCDprovided by HGNC
    Official Full Name
    sarcoglycan deltaprovided by HGNC
    Primary source
    HGNC:HGNC:10807
    See related
    Ensembl:ENSG00000170624 MIM:601411; Vega:OTTHUMG00000163445
    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

    Genomic context

    See SGCD in Genome Data Viewer
    Location:
    5q33.2-q33.3
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    109 current GRCh38.p12 (GCF_000001405.38) 5 NC_000005.10 (155728636..156767788)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (155462147..156194799)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene STN1, CST complex subunit pseudogene Neighboring gene peptidylprolyl isomerase G pseudogene 1 Neighboring gene RNA, 5S ribosomal pseudogene 199 Neighboring gene uncharacterized LOC105377673 Neighboring gene RNA, U6 small nuclear 556, pseudogene Neighboring gene PPP1R2 family member B

    Genomic regions, transcripts, and products

    Expression

    • Project title: 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 Jun 15 11:32:44 2016

    Bibliography

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Phenotypes

    NHGRI GWAS Catalog

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

    Pathways from BioSystems

    • Arrhythmogenic Right Ventricular Cardiomyopathy, organism-specific biosystem (from WikiPathways)
      Arrhythmogenic Right Ventricular Cardiomyopathy, organism-specific biosystemAdapted from KEGG: http://www.genome.jp/kegg/pathway/hsa/hsa05412.html
    • Arrhythmogenic right ventricular cardiomyopathy (ARVC), organism-specific biosystem (from KEGG)
      Arrhythmogenic right ventricular cardiomyopathy (ARVC), organism-specific biosystemArrhythmogenic right ventricular cardiomyopathy (ARVC) is an inherited heart muscle disease that may result in arrhythmia, heart failure, and sudden death. The hallmark pathological findings are prog...
    • Arrhythmogenic right ventricular cardiomyopathy (ARVC), conserved biosystem (from KEGG)
      Arrhythmogenic right ventricular cardiomyopathy (ARVC), conserved biosystemArrhythmogenic right ventricular cardiomyopathy (ARVC) is an inherited heart muscle disease that may result in arrhythmia, heart failure, and sudden death. The hallmark pathological findings are prog...
    • Dilated cardiomyopathy, organism-specific biosystem (from KEGG)
      Dilated cardiomyopathy, organism-specific biosystemDilated cardiomyopathy (DCM) is a heart muscle disease characterised by dilation and impaired contraction of the left or both ventricles that results in progressive heart failure and sudden cardiac d...
    • Dilated cardiomyopathy, conserved biosystem (from KEGG)
      Dilated cardiomyopathy, conserved biosystemDilated cardiomyopathy (DCM) is a heart muscle disease characterised by dilation and impaired contraction of the left or both ventricles that results in progressive heart failure and sudden cardiac d...
    • Hypertrophic cardiomyopathy (HCM), organism-specific biosystem (from KEGG)
      Hypertrophic cardiomyopathy (HCM), organism-specific biosystemHypertrophic cardiomyopathy (HCM) is a primary myocardial disorder with an autosomal dominant pattern of inheritance that is characterized by hypertrophy of the left ventricles with histological feat...
    • Hypertrophic cardiomyopathy (HCM), conserved biosystem (from KEGG)
      Hypertrophic cardiomyopathy (HCM), conserved biosystemHypertrophic cardiomyopathy (HCM) is a primary myocardial disorder with an autosomal dominant pattern of inheritance that is characterized by hypertrophy of the left ventricles with histological feat...
    • Viral myocarditis, organism-specific biosystem (from KEGG)
      Viral myocarditis, organism-specific biosystemMyocarditis is a cardiac disease associated with inflammation and injury of the myocardium. It results from various etiologies, both noninfectious and infectious, but coxsackievirus B3 (CVB3) is stil...

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • MGC22567

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    heart contraction IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    muscle organ development TAS
    Traceable Author Statement
    more info
    PubMed 
    Component Evidence Code Pubs
    cytoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    cytoskeleton IEA
    Inferred from Electronic Annotation
    more info
     
    dystrophin-associated glycoprotein complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    integral component of membrane IEA
    Inferred from Electronic Annotation
    more info
     
    plasma membrane TAS
    Traceable Author Statement
    more info
    PubMed 
    sarcoglycan complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    sarcolemma IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 

    General protein information

    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)

    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_000337.5NP_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, OTTHUMP00000223947, ENST00000337851.8, OTTHUMT00000373470
      Conserved Domains (1) summary
      pfam04790
      Location:24278
      Sarcoglycan_1; Sarcoglycan complex subunit protein
    2. NM_001128209.1NP_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
      Q92629
      Related
      ENSP00000403003.2, OTTHUMP00000223946, ENST00000435422.7, OTTHUMT00000373469
      Conserved Domains (1) summary
      pfam04790
      Location:23277
      Sarcoglycan_1; Sarcoglycan complex subunit protein
    3. NM_172244.2NP_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, OTTHUMP00000223961, ENST00000517913.5, OTTHUMT00000373502
      Conserved Domains (1) summary
      pfam04790
      Location:29235
      Sarcoglycan_1; Sarcoglycan complex subunit protein

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

    Reference GRCh38.p12 Primary Assembly

    Genomic

    1. NC_000005.10 Reference GRCh38.p12 Primary Assembly

      Range
      155728636..156767788
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017009724.1XP_016865213.1  delta-sarcoglycan isoform X1

      UniProtKB/Swiss-Prot
      Q92629
      Conserved Domains (1) summary
      pfam04790
      Location:24278
      Sarcoglycan_1; Sarcoglycan complex subunit protein
    2. XM_017009723.2XP_016865212.1  delta-sarcoglycan isoform X1

      UniProtKB/Swiss-Prot
      Q92629
      Conserved Domains (1) summary
      pfam04790
      Location:24278
      Sarcoglycan_1; Sarcoglycan complex subunit protein
    3. XM_011534621.2XP_011532923.1  delta-sarcoglycan isoform X2

      See identical proteins and their annotated locations for XP_011532923.1

      UniProtKB/Swiss-Prot
      Q92629
      Conserved Domains (1) summary
      pfam04790
      Location:23277
      Sarcoglycan_1; Sarcoglycan complex subunit protein
    4. XM_005265967.2XP_005266024.1  delta-sarcoglycan isoform X3

      Conserved Domains (1) summary
      pfam04790
      Location:29166
      Sarcoglycan_1; Sarcoglycan complex subunit protein
    5. XM_005265966.5XP_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:24278
      Sarcoglycan_1; Sarcoglycan complex subunit protein
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