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

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: mouse all
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Genomic context

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_000021.9 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Dysfunction of NMDA receptors in neuronal models of an autism spectrum disorder patient with a DSCAM mutation and in Dscam-knockout mice.
Title: Dysfunction of NMDA receptors in neuronal models of an autism spectrum disorder patient with a DSCAM mutation and in Dscam-knockout mice.
Long non-coding RNA Down syndrome cell adhesion molecule-anti-sense 1 promotes gastric carcinoma cell proliferation and migration by regulating the miR-204/TPT1 axis.
Title: Long non-coding RNA Down syndrome cell adhesion molecule-anti-sense 1 promotes gastric carcinoma cell proliferation and migration by regulating the miR-204/TPT1 axis.
DSCAM/PAK1 pathway suppression reverses neurogenesis deficits in iPSC-derived cerebral organoids from patients with Down syndrome.
Title: DSCAM/PAK1 pathway suppression reverses neurogenesis deficits in iPSC-derived cerebral organoids from patients with Down syndrome.
Role of DSCAM in the Development of Neural Control of Movement and Locomotion.
Title: Role of DSCAM in the Development of Neural Control of Movement and Locomotion.
Long non-coding RNA DSCAM-AS1 contributes to the tumorigenesis of cervical cancer by targeting miR-877-5p/ATXN7L3 axis.
Title: Long non-coding RNA DSCAM-AS1 contributes to the tumorigenesis of cervical cancer by targeting miR-877-5p/ATXN7L3 axis.
We further show that introns drive selection of both proximal and distal variable exons. Since exon 4 cluster introns lack conserved sequences that could mediate robust long-range base-pairing to bring exons into proximity for splicing, our data argue for a central role of introns in mutually exclusive alternative splicing of Dscam exon 4 cluster
Title: Plasmid-based gap-repair recombineered transgenes reveal a central role for introns in mutually exclusive alternative splicing in Down Syndrome Cell Adhesion Molecule exon 4.
There is an association between DSCAM polymorphisms and non-syndromic HSCR in South Chinese population.
Title: Association between DSCAM polymorphisms and non-syndromic Hirschsprung disease in Chinese population.
Genome wide analysis identified DSCAM as a new imprinted gene in the human placenta.
Title: A genome-wide search for new imprinted genes in the human placenta identifies DSCAM as the first imprinted gene on chromosome 21.
Our study did not repeatedly confirm the association of the rs2222973 or the rs11770843 SNP with adolescent idiopathic scoliosis in a Chinese Han population.
Title: Lack of association between DSCAM gene polymorphisms and adolescent idiopathic scoliosis susceptibility in a Chinese Han population.
The most significant was DSCAM, a neurological gene expressed widely in the developing brain and in the amygdala and hippocampus of the adult brain.
Title: An analysis of gene expression in PTSD implicates genes involved in the glucocorticoid receptor pathway and neural responses to stress.

Submit: New GeneRIF Correction See all GeneRIFs (27)

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

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

PMC310729P5 (e-PCR)
- UniSTS:272654

SHGC-6872 (e-PCR)
- UniSTS:87312

D21S348 (e-PCR)
- UniSTS:147732

D21S349 (e-PCR)
- UniSTS:147733

SHGC-52084 (e-PCR)
- UniSTS:73261

G29038 (e-PCR)
- UniSTS:12589

G29042 (e-PCR)
- UniSTS:80953

G43599 (e-PCR)
- UniSTS:95036

SHGC-152951 (e-PCR)
- UniSTS:185161

G48509 (e-PCR)
- UniSTS:95569

SHGC-51874 (e-PCR)
- UniSTS:68705

STS-U44101 (e-PCR)
- UniSTS:61798

DSCAM__4776 (e-PCR)
- UniSTS:471422

SHGC-51860 (e-PCR)
- UniSTS:75648

SHGC-11765 (e-PCR)
- UniSTS:75649

G29050 (e-PCR)
- UniSTS:67973

SHGC-144799 (e-PCR)
- UniSTS:172423

G29047 (e-PCR)
- UniSTS:9353

D5S1845 (e-PCR)
- UniSTS:39565

D21S1806 (e-PCR)
- UniSTS:32660

SHGC-53823 (e-PCR)
- UniSTS:63639

SHGC-52082 (e-PCR)
- UniSTS:71576

SHGC-6874 (e-PCR)
- UniSTS:84124

G34687 (e-PCR)
- UniSTS:72094

D21S1840 (e-PCR)
- UniSTS:1441

SHGC-77994 (e-PCR)
- UniSTS:101538

D21S1887 (e-PCR), detects polymorphism
- UniSTS:25510

RH68680 (e-PCR)
- UniSTS:76201

D21S15 (e-PCR)
- UniSTS:147881

SHGC-144335 (e-PCR)
- UniSTS:172201

D21S23 (e-PCR)
- UniSTS:147885

D21S1889 (e-PCR)
- UniSTS:63425

SHGC-144398 (e-PCR)
- UniSTS:172233

SHGC-87651 (e-PCR)
- UniSTS:51411

G59520 (e-PCR)
- UniSTS:136683

D21S1965 (e-PCR)
- UniSTS:52980

D21S1906 (e-PCR), detects polymorphism
- UniSTS:44280

D21S1729E (e-PCR)
- UniSTS:150783

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

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Preferred Names: cell adhesion molecule DSCAM

Names: Down syndrome cell adhesion molecule

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.

mRNA and Protein(s)

NM_001271534.3 → NP_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:424 → 493

Ig; Immunoglobulin domain

cd05734
Location:707 → 784

Ig7_DSCAM; Seventh immunoglobulin (Ig)-like domain of Down Syndrome Cell Adhesion molecule (DSCAM)

smart00408
Location:239 → 300

IGc2; Immunoglobulin C-2 Type

smart00409
Location:44 → 113

IG; Immunoglobulin

smart00410
Location:236 → 310

IG_like; Immunoglobulin like

cd00063
Location:1380 → 1470

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:690 → 784

I-set; Immunoglobulin I-set domain

cl11960
Location:802 → 889

Ig; Immunoglobulin domain
NM_001389.5 → NP_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:707 → 784

Ig_DSCAM; Immunoglobulin (Ig)-like domain of Down Syndrome Cell Adhesion molecule (DSCAM)

smart00408
Location:518 → 575

IGc2; Immunoglobulin C-2 Type

cd00063
Location:1380 → 1470

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:235 → 310

I-set; Immunoglobulin I-set domain

pfam13927
Location:407 → 488

Ig_3; Immunoglobulin domain

cd00096
Location:1303 → 1369

Ig; Immunoglobulin domain

cl11960
Location:802 → 889

Ig; Immunoglobulin domain

cl28434
Location:596 → 686

I-set; Immunoglobulin I-set domain

RNA

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

NC_000021.9 Reference GRCh38.p14 Primary Assembly

Range

40010999..40847158 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

Q8WY19

Related

ENSP00000478698.1, ENST00000617870.4

Conserved Domains (7) summary

cd00096
Location:188 → 257

Ig; Immunoglobulin domain

cd05734
Location:471 → 548

Ig7_DSCAM; Seventh immunoglobulin (Ig)-like domain of Down Syndrome Cell Adhesion molecule (DSCAM)

smart00408
Location:3 → 64

IGc2; Immunoglobulin C-2 Type

smart00410
Location:1 → 74

IG_like; Immunoglobulin like

cd00063
Location:1144 → 1234

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:454 → 548

I-set; Immunoglobulin I-set domain

cl11960
Location:566 → 653

Ig; Immunoglobulin domain