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

    Gene ID: 9993, updated on 10-Dec-2024

    Summary

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    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

    Expression

    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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

    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)

    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_001173533.2NP_001167004.1  integral membrane protein DGCR2/IDD isoform 2 precursor

      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:74226
      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:230291
      VWC; von Willebrand factor (vWF) type C domain
      pfam04534
      Location:385433
      Herpes_UL56; Herpesvirus UL56 protein
    2. NM_001173534.2NP_001167005.1  integral membrane protein DGCR2/IDD isoform 3 precursor

      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:71223
      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:227288
      VWC; von Willebrand factor (vWF) type C domain
      pfam04534
      Location:382430
      Herpes_UL56; Herpesvirus UL56 protein
    3. NM_001184781.2NP_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:112264
      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:268326
      VWC; von Willebrand factor (vWF) type C domain
      cd00112
      Location:3066
      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:420459
      Extensin_2; Extensin-like region
    4. NM_005137.3NP_005128.1  integral membrane protein DGCR2/IDD isoform 1 precursor

      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:115267
      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:271329
      VWC; von Willebrand factor (vWF) type C domain
      PHA03247
      Location:428537
      PHA03247; large tegument protein UL36; Provisional
      cd00112
      Location:3066
      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)