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

Gene ID: 1826, updated on 17-Jun-2019

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
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

Genomic context

See DSCAM in Genome Data Viewer
Location:
21q22.2
Exon count:
33
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 21 NC_000021.9 (40010999..40847158, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (41384343..42219039, complement)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene meiotic recombination hotspot PCP4-1 Neighboring gene meiotic recombination hotspot PCP4-2 Neighboring gene Purkinje cell protein 4 Neighboring gene microRNA 4760 Neighboring gene uncharacterized LOC105369294 Neighboring gene DSCAM antisense RNA 1 Neighboring gene DSCAM intronic transcript 1 Neighboring gene yrdC N(6)-threonylcarbamoyltransferase domain containing pseudogene 3 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 FunctionsWhat's a GeneRIF?

Phenotypes

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2018-01-24)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated (2018-01-24)

ClinGen Genome Curation PagePubMed

NHGRI GWAS Catalog

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

Pathways from BioSystems

  • Cell-Cell communication, organism-specific biosystem (from REACTOME)
    Cell-Cell communication, organism-specific biosystemCell-to-Cell communication is crucial for multicellular organisms because it allows organisms to coordinate the activity of their cells. Some cell-to-cell communication requires direct cell-cell cont...
  • DSCAM interactions, organism-specific biosystem (from REACTOME)
    DSCAM interactions, organism-specific biosystemDSCAM (Down syndrome cell adhesion molecule) is one of the members of the Ig superfamily CAMs with a domain architecture comprising 10 Ig domains, 6 fibronectin type III (FN) repeats, a single transm...
  • FOXA1 transcription factor network, organism-specific biosystem (from Pathway Interaction Database)
    FOXA1 transcription factor network, organism-specific biosystem
    FOXA1 transcription factor network

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

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

General protein information

Preferred Names
Down syndrome cell adhesion molecule

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.

mRNA and Protein(s)

  1. NM_001271534.3NP_001258463.1  Down syndrome cell adhesion molecule 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
    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  Down syndrome cell adhesion molecule 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
    O60469
    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_073202.2 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, AF064862, AF217525, BM684380

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000021.9 Reference GRCh38.p13 Primary Assembly

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

mRNA and Protein(s)

  1. XM_017028281.1XP_016883770.1  Down syndrome cell adhesion molecule isoform X1

    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
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