U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

DGCR2 DiGeorge syndrome critical region gene 2 [ Homo sapiens (human) ]

Gene ID: 9993, updated on 5-Mar-2024

Summary

Go to the top of the page Help
Official Symbol
DGCR2provided by HGNC
Official Full Name
DiGeorge syndrome critical region gene 2provided by HGNC
Primary source
HGNC:HGNC:2845
See related
Ensembl:ENSG00000070413 MIM:600594; AllianceGenome:HGNC:2845
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
IDD; LAN; DGS-C; SEZ-12
Summary
Deletions of the 22q11.2 have been associated with a wide range of developmental defects (notably DiGeorge syndrome, velocardiofacial syndrome, conotruncal anomaly face syndrome and isolated conotruncal cardiac defects) classified under the acronym CATCH 22. The DGCR2 gene encodes a novel putative adhesion receptor protein, which could play a role in neural crest cells migration, a process which has been proposed to be altered in DiGeorge syndrome. Alternative splicing results in multiple transcript variants.[provided by RefSeq, May 2010]
Expression
Ubiquitous expression in brain (RPKM 24.0), skin (RPKM 23.8) and 25 other tissues See more
Orthologs
mouse all
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See DGCR2 in Genome Data Viewer
Location:
22q11.21
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (19036286..19122412, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (19411609..19497031, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (19023799..19109925, complement)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene DiGeorge syndrome critical region gene 5 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13451 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19024185-19024805 Neighboring gene family with sequence similarity 246 member C (gene/pseudogene) Neighboring gene CA15 pseudogene 1 Neighboring gene DiGeorge syndrome critical region gene 11 Neighboring gene ribosomal protein L28 pseudogene 6 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19073555-19074056 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19074057-19074556 Neighboring gene uncharacterized LOC124905078 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19093647-19094147 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13452 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19097371-19097873 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19097874-19098375 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:19101726-19102620 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:19109284-19109785 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13454 Neighboring gene testis specific serine kinase 1A (pseudogene) Neighboring gene testis specific serine kinase 2 Neighboring gene ess-2 splicing factor homolog

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • 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

Go to the top of the pageHelp

Related articles in PubMed

  1. DGCR2 influences cortical thickness through a mechanism independent of schizophrenia pathogenesis. Belangero SI, et al. Psychiatry Res, 2019 Apr. PMID 30901624
  2. No association between genetic variants at the DGCR2 gene and schizophrenia in a German sample. Georgi A, et al. Psychiatr Genet, 2009 Apr. PMID 19668116
  3. A complete genetic association scan of the 22q11 deletion region and functional evidence reveal an association between DGCR2 and schizophrenia. Shifman S, et al. Hum Genet, 2006 Sep. PMID 16783572
  4. Isolation of a gene encoding an integral membrane protein from the vicinity of a balanced translocation breakpoint associated with DiGeorge syndrome. Wadey R, et al. Hum Mol Genet, 1995 Jun. PMID 7655455
  5. Cloning of a balanced translocation breakpoint in the DiGeorge syndrome critical region and isolation of a novel potential adhesion receptor gene in its vicinity. Demczuk S, et al. Hum Mol Genet, 1995 Apr. PMID 7633403

See all (34) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. While no association between DGCR2 polymorphisms and schizophrenia was found, the missense variant rs2072123 was associated to left rostral anterior cingulate thickness, showing that DGCR2 seems not to be associated directly with the schizophrenia but might be influencing the brain morphology. We also showed a DGCR2 downregulation in schizophrenia patients when compared to controls and first episode of psychosis.
    Title: DGCR2 influences cortical thickness through a mechanism independent of schizophrenia pathogenesis.
  2. DGCR2, GPR44 and SerpinB10, found in beta cells, were negative in all other cell types within pancreas and exposed epitopes at the cell surface
    Title: Novel pancreatic beta cell-specific proteins: antibody-based proteomics for identification of new biomarker candidates.
  3. These data do not support a significant role of DGCR2 in the aetiology of schizophrenia in the German population.
    Title: No association between genetic variants at the DGCR2 gene and schizophrenia in a German sample.
  4. Observational study of gene-disease association. (HuGE Navigator)
    Title: No association between genetic variants at the DGCR2 gene and schizophrenia in a German sample.
  5. Study confirmed the association between DGCR2 & schizophrenia through genotyping of 1,400 subjects; in a gene expression analysis, the risk allele of a coding SNP associated with schizophrenia was found to be associated with a reduced expression of DGCR2.
    Title: A complete genetic association scan of the 22q11 deletion region and functional evidence reveal an association between DGCR2 and schizophrenia.
Submit: New GeneRIF Correction

Phenotypes

Go to the top of the page Help

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Velocardiofacial syndrome
MedGen: C0220704 OMIM: 192430 GeneReviews: 22q11.2 Deletion Syndrome
Compare labs

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

Go to the top of the page

Interactions

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

Markers

Homology

Clone Names

  • KIAA0163, DKFZp686I1730

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables carbohydrate binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in animal organ morphogenesis TAS
Traceable Author Statement
more info
 PubMed 
involved_in cell adhesion IEA
Inferred from Electronic Annotation
more info
  
involved_in cognition IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
is_active_in membrane IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

Go to the top of the page Help
Preferred Names
integral membrane protein DGCR2/IDD
Names
DiGeorge syndrome critical region protein 2
integral membrane protein deleted in DiGeorge syndrome

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

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_021333.2 RefSeqGene

    Range
    5043..91169
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001173533.2 → NP_001167004.1  integral membrane protein DGCR2/IDD isoform 2 precursor

    See identical proteins and their annotated locations for NP_001167004.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1. The resulting isoform (2) lacks an internal segment, compared to isoform 1.
    Source sequence(s)
    AK304382, BC040500
    Consensus CDS
    CCDS54496.1
    UniProtKB/TrEMBL
    B7Z3T5
    Related
    ENSP00000440062.1, ENST00000537045.5
    Conserved Domains (3) summary
    cd03599
    Location:74 → 226
    CLECT_DGCR2_like; C-type lectin-like domain (CTLD) of the type found in DGCR2, an integral membrane protein deleted in DiGeorge Syndrome (DGS)
    smart00214
    Location:230 → 291
    VWC; von Willebrand factor (vWF) type C domain
    pfam04534
    Location:385 → 433
    Herpes_UL56; Herpesvirus UL56 protein

  2. NM_001173534.2 → NP_001167005.1  integral membrane protein DGCR2/IDD isoform 3 precursor

    See identical proteins and their annotated locations for NP_001167005.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an alternate in-frame exon and uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. The resulting isoform (3) lacks two internal segments, compared to isoform 1.
    Source sequence(s)
    AK296337, BC032430, BC040500, DA494775
    UniProtKB/TrEMBL
    B7Z3T5
    Conserved Domains (3) summary
    cd03599
    Location:71 → 223
    CLECT_DGCR2_like; C-type lectin-like domain (CTLD) of the type found in DGCR2, an integral membrane protein deleted in DiGeorge Syndrome (DGS)
    smart00214
    Location:227 → 288
    VWC; von Willebrand factor (vWF) type C domain
    pfam04534
    Location:382 → 430
    Herpes_UL56; Herpesvirus UL56 protein

  3. NM_001184781.2 → NP_001171710.1  integral membrane protein DGCR2/IDD isoform 4 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. The resulting isoform (4) lacks a short internal segment, compared to isoform 1.
    Source sequence(s)
    AK296337, CR936871, DA494775
    UniProtKB/TrEMBL
    F6SYP7
    Conserved Domains (4) summary
    cd03599
    Location:112 → 264
    CLECT_DGCR2_like; C-type lectin-like domain (CTLD) of the type found in DGCR2, an integral membrane protein deleted in DiGeorge Syndrome (DGS)
    smart00214
    Location:268 → 326
    VWC; von Willebrand factor (vWF) type C domain
    cd00112
    Location:30 → 66
    LDLa; Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about ...
    pfam04554
    Location:420 → 459
    Extensin_2; Extensin-like region

  4. NM_005137.3 → NP_005128.1  integral membrane protein DGCR2/IDD isoform 1 precursor

    See identical proteins and their annotated locations for NP_005128.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    BC040500, D79985, DA494775
    Consensus CDS
    CCDS33598.1
    UniProtKB/Swiss-Prot
    A6NIB5, A8K6K5, B5TY34, B7Z935, P98153
    UniProtKB/TrEMBL
    Q8IWC8
    Related
    ENSP00000263196.7, ENST00000263196.12
    Conserved Domains (4) summary
    cd03599
    Location:115 → 267
    CLECT_DGCR2_like; C-type lectin-like domain (CTLD) of the type found in DGCR2, an integral membrane protein deleted in DiGeorge Syndrome (DGS)
    smart00214
    Location:271 → 329
    VWC; von Willebrand factor (vWF) type C domain
    PHA03247
    Location:428 → 537
    PHA03247; large tegument protein UL36; Provisional
    cd00112
    Location:30 → 66
    LDLa; Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about ...

RNA

  1. NR_033674.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks an alternate in-frame exon and uses an alternate in-frame splice site in the 5' coding region, compared to variant 1, which results in a frameshift and early stop codon. The transcript is sufficiently abundant to represent as a RefSeq record; however, the predicted protein is not represented because the product is significantly truncated and the transcript is a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK295697, CR936871
    Related
    ENST00000389262.8

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_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    19036286..19122412 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    19411609..19497031 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P98153.1 GenPept UniProtKB/Swiss-Prot:P98153

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information
Molecular Biology Databases
Research Materials
Tools
Miscellaneous