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    DSCAM DS cell adhesion molecule [ Homo sapiens (human) ]

    Gene ID: 1826, updated on 17-Jun-2024

    Summary

    Official Symbol
    DSCAMprovided by HGNC
    Official Full Name
    DS cell adhesion moleculeprovided by HGNC
    Primary source
    HGNC:HGNC:3039
    See related
    Ensembl:ENSG00000171587 MIM:602523; AllianceGenome:HGNC:3039
    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
    CHD2; CHD2-42; CHD2-52
    Summary
    This gene is a member of the immunoglobulin superfamily of cell adhesion molecules (Ig-CAMs), and is involved in human central and peripheral nervous system development. This gene is a candidate for Down syndrome and congenital heart disease (DSCHD). A gene encoding a similar Ig-CAM protein is located on chromosome 11. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Oct 2012]
    Expression
    Biased expression in brain (RPKM 4.3), spleen (RPKM 0.3) and 2 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See DSCAM in Genome Data Viewer
    Location:
    21q22.2
    Exon count:
    33
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (40010999..40847158, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (38398213..39235595, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (41382926..42219084, complement)

    Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr21:41150548-41151747 Neighboring gene uncharacterized LOC107985500 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:41184118-41184339 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr21:41217248-41218447 Neighboring gene immunoglobulin superfamily member 5 Neighboring gene NANOG hESC enhancer GRCh37_chr21:41223988-41224489 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:41241262-41241415 Neighboring gene meiotic recombination hotspot PCP4-1 Neighboring gene meiotic recombination hotspot PCP4-2 Neighboring gene MPRA-validated peak4411 silencer Neighboring gene Purkinje cell protein 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:41400415-41400914 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:41436401-41436568 Neighboring gene NANOG hESC enhancer GRCh37_chr21:41474546-41475047 Neighboring gene microRNA 4760 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr21:41709903-41711102 Neighboring gene uncharacterized LOC105369294 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr21:41792223-41793422 Neighboring gene DSCAM antisense RNA 1 Neighboring gene small nucleolar RNA SNORA51 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr21:41919896-41920505 Neighboring gene NANOG hESC enhancer GRCh37_chr21:41959554-41960078 Neighboring gene NANOG hESC enhancer GRCh37_chr21:41995355-41995997 Neighboring gene DSCAM intronic transcript 1 Neighboring gene uncharacterized LOC124905066 Neighboring gene NANOG hESC enhancer GRCh37_chr21:42241274-42241775 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:42296237-42296738 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:42296739-42297238 Neighboring gene NANOG hESC enhancer GRCh37_chr21:42306817-42307318 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr21:42308234-42309433 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr21:42326589-42327160 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr21:42331949-42332650 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr21:42339602-42340102 Neighboring gene yrdC N(6)-threonylcarbamoyltransferase domain containing pseudogene 3 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr21:42424381-42425580 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:42474333-42474833 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:42513074-42513270 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr21:42519321-42519905 Neighboring gene long intergenic non-protein coding RNA 323

    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

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2023-10-10)

    ClinGen Genome Curation Page
    Haploinsufficency

    Some evidence for dosage pathogenicity (Last evaluated 2023-10-10)

    ClinGen Genome Curation PagePubMed

    EBI GWAS Catalog

    Description
    Common variation near ROBO2 is associated with expressive vocabulary in infancy.
    EBI GWAS Catalog
    Duffy-null-associated low neutrophil counts influence HIV-1 susceptibility in high-risk South African black women.
    EBI GWAS Catalog
    Genome-wide association study of ancestry-specific TB risk in the South African Coloured population.
    EBI GWAS Catalog
    Genome-wide association study of co-occurring anxiety in major depression.
    EBI GWAS Catalog
    Genome-wide association study on overall survival of advanced non-small cell lung cancer patients treated with carboplatin and paclitaxel.
    EBI GWAS Catalog
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    EBI GWAS Catalog
    TSPYL5 SNPs: association with plasma estradiol concentrations and aromatase expression.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables cell-cell adhesion mediator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables netrin receptor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein tyrosine kinase binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    involved_in axon guidance IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in axon guidance ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in camera-type eye photoreceptor cell differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in cell adhesion TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in central nervous system development IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in dendrite morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in dendrite self-avoidance IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in dendrite self-avoidance ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in homophilic cell adhesion via plasma membrane adhesion molecules IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in homophilic cell adhesion via plasma membrane adhesion molecules ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in locomotory behavior IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of cell adhesion ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in nervous system development TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in netrin-activated signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of axon extension involved in axon guidance IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in positive regulation of axon extension involved in axon guidance IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of phosphorylation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in post-embryonic retina morphogenesis in camera-type eye IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in retina layer formation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in synapse assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Component Evidence Code Pubs
    is_active_in axon IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in axon ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in dendrite ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
     
    located_in growth cone ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in membrane TAS
    Traceable Author Statement
    more info
    PubMed 
    is_active_in neuronal cell body IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in neuronal cell body ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
     
    located_in synapse ISS
    Inferred from Sequence or Structural Similarity
    more info
     

    General protein information

    Preferred Names
    cell adhesion molecule DSCAM
    Names
    Down syndrome cell adhesion molecule

    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.

    mRNA and Protein(s)

    1. NM_001271534.3NP_001258463.1  cell adhesion molecule DSCAM isoform 2 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. This results in a shorter protein (isoform 2), compared to isoform CHD2-42.
      Source sequence(s)
      AF023449, AF043945, AF064862, AF289030, BM684380
      UniProtKB/TrEMBL
      Q59GH3
      Conserved Domains (8) summary
      cd00096
      Location:424493
      Ig; Immunoglobulin domain
      cd05734
      Location:707784
      Ig7_DSCAM; Seventh immunoglobulin (Ig)-like domain of Down Syndrome Cell Adhesion molecule (DSCAM)
      smart00408
      Location:239300
      IGc2; Immunoglobulin C-2 Type
      smart00409
      Location:44113
      IG; Immunoglobulin
      smart00410
      Location:236310
      IG_like; Immunoglobulin like
      cd00063
      Location:13801470
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      pfam07679
      Location:690784
      I-set; Immunoglobulin I-set domain
      cl11960
      Location:802889
      Ig; Immunoglobulin domain
    2. NM_001389.5NP_001380.2  cell adhesion molecule DSCAM isoform CHD2-42 precursor

      See identical proteins and their annotated locations for NP_001380.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (CHD2-42).
      Source sequence(s)
      AF043945, AF064862, AF217525, BE503065, BM684380
      Consensus CDS
      CCDS42929.1
      UniProtKB/Swiss-Prot
      O60468, O60469
      UniProtKB/TrEMBL
      Q59GH3
      Related
      ENSP00000383303.1, ENST00000400454.6
      Conserved Domains (8) summary
      cd05734
      Location:707784
      Ig_DSCAM; Immunoglobulin (Ig)-like domain of Down Syndrome Cell Adhesion molecule (DSCAM)
      smart00408
      Location:518575
      IGc2; Immunoglobulin C-2 Type
      cd00063
      Location:13801470
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      pfam07679
      Location:235310
      I-set; Immunoglobulin I-set domain
      pfam13927
      Location:407488
      Ig_3; Immunoglobulin domain
      cd00096
      Location:13031369
      Ig; Immunoglobulin domain
      cl11960
      Location:802889
      Ig; Immunoglobulin domain
      cl28434
      Location:596686
      I-set; Immunoglobulin I-set domain

    RNA

    1. NR_073202.3 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate splice site in an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AF023450, AF043945, AF064862, AF217525, BM684380

    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_000021.9 Reference GRCh38.p14 Primary Assembly

      Range
      40010999..40847158 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017028281.2XP_016883770.1  cell adhesion molecule DSCAM isoform X1

      UniProtKB/TrEMBL
      Q8WY19
      Related
      ENSP00000478698.1, ENST00000617870.4
      Conserved Domains (7) summary
      cd00096
      Location:188257
      Ig; Immunoglobulin domain
      cd05734
      Location:471548
      Ig7_DSCAM; Seventh immunoglobulin (Ig)-like domain of Down Syndrome Cell Adhesion molecule (DSCAM)
      smart00408
      Location:364
      IGc2; Immunoglobulin C-2 Type
      smart00410
      Location:174
      IG_like; Immunoglobulin like
      cd00063
      Location:11441234
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      pfam07679
      Location:454548
      I-set; Immunoglobulin I-set domain
      cl11960
      Location:566653
      Ig; Immunoglobulin domain

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_025791814.1 Reference GRCh38.p14 PATCHES

      Range
      150307..986812 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054333308.1XP_054189283.1  cell adhesion molecule DSCAM isoform X1

      UniProtKB/TrEMBL
      Q8WY19

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060945.1 Alternate T2T-CHM13v2.0

      Range
      38398213..39235595 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054324369.1XP_054180344.1  cell adhesion molecule DSCAM isoform X2

      UniProtKB/TrEMBL
      A0A087WUI7