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

    Gene ID: 9993, updated on 27-Nov-2024

    Summary

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    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
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    Genomic context

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    See DGCR2 in Genome Data Viewer
    Location:
    22q11.21
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (19036286..19122412, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (19411609..19497031, complement)
    RS_2024_09 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

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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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    Related articles in PubMed

    1. DiGeorge syndrome and 22q11 rearrangements. Augusseau S, et al. Hum Genet, 1986 Oct. PMID 3770751
    2. 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
    3. 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
    4. 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
    5. 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

    See all (37) 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

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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

    Associated conditions

    Description Tests
    Velocardiofacial syndrome
    MedGen: C0220704 OMIM: 192430 GeneReviews: 22q11.2 Deletion Syndrome
    		not available

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    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

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    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)

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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.

    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
      Q8IWC8
      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_2024_08

    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.

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