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    SGCD sarcoglycan delta [ Homo sapiens (human) ]

    Gene ID: 6444, updated on 5-Mar-2024

    Summary

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SGCD in Genome Data Viewer
    Location:
    5q33.2-q33.3
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (155727832..156767788)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (156261684..157286763)
    105.20220307 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

    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 Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    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 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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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

    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)

    NEW Try the new Transcript table

    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_000337.6NP_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:24278
      Sarcoglycan_1; Sarcoglycan complex subunit protein
    2. NM_001128209.2NP_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:23277
      Sarcoglycan_1; Sarcoglycan complex subunit protein
    3. NM_172244.3NP_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:29235
      Sarcoglycan_1; Sarcoglycan complex subunit protein

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    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_047417519.1XP_047273475.1  delta-sarcoglycan isoform X1

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

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

      UniProtKB/Swiss-Prot
      Q92629
      Conserved Domains (1) summary
      pfam04790
      Location:24278
      Sarcoglycan_1; Sarcoglycan complex subunit protein
    4. XM_047417520.1XP_047273476.1  delta-sarcoglycan isoform X2

      UniProtKB/Swiss-Prot
      A8K9S9, Q53XA5, Q92629, Q99644
    5. XM_005265967.3XP_005266024.1  delta-sarcoglycan isoform X3

      Conserved Domains (1) summary
      pfam04790
      Location:29166
      Sarcoglycan_1; Sarcoglycan complex subunit protein
    6. XM_005265966.6XP_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

    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_054353130.1XP_054209105.1  delta-sarcoglycan isoform X1

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

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

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

      UniProtKB/Swiss-Prot
      A8K9S9, Q53XA5, Q92629, Q99644
    5. XM_054353132.1XP_054209107.1  delta-sarcoglycan isoform X3

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