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CD19 CD19 molecule [ Homo sapiens (human) ]

Gene ID: 930, updated on 9-Aug-2021

Summary

Official Symbol
CD19provided by HGNC
Official Full Name
CD19 moleculeprovided by HGNC
Primary source
HGNC:HGNC:1633
See related
Ensembl:ENSG00000177455 MIM:107265
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
B4; CVID3
Summary
This gene encodes a member of the immunoglobulin gene superfamily. Expression of this cell surface protein is restricted to B cell lymphocytes. This protein is a reliable marker for pre-B cells but its expression diminishes during terminal B cell differentiation in antibody secreting plasma cells. The protein has two N-terminal extracellular Ig-like domains separated by a non-Ig-like domain, a hydrophobic transmembrane domain, and a large C-terminal cytoplasmic domain. This protein forms a complex with several membrane proteins including complement receptor type 2 (CD21) and tetraspanin (CD81) and this complex reduces the threshold for antigen-initiated B cell activation. Activation of this B-cell antigen receptor complex activates the phosphatidylinositol 3-kinase signalling pathway and the subsequent release of intracellular stores of calcium ions. This protein is a target of chimeric antigen receptor (CAR) T-cells used in the treatment of lymphoblastic leukemia. Mutations in this gene are associated with the disease common variable immunodeficiency 3 (CVID3) which results in a failure of B-cell differentiation and impaired secretion of immunoglobulins. CVID3 is characterized by hypogammaglobulinemia, an inability to mount an antibody response to antigen, and recurrent bacterial infections. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jul 2020]
Annotation information
Note: This gene has been reviewed for its involvement in coronavirus biology, and is involved in immune response or antiviral activity.
Expression
Biased expression in lymph node (RPKM 43.1), spleen (RPKM 28.3) and 3 other tissues See more
Orthologs
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Genomic context

See CD19 in Genome Data Viewer
Location:
16p11.2
Exon count:
15
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 16 NC_000016.10 (28931735..28939347)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (28943292..28950663)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene ATP2A1 antisense RNA 1 Neighboring gene ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 1 Neighboring gene rabaptin, RAB GTPase binding effector protein 2 Neighboring gene nuclear factor of activated T cells 2 interacting protein Neighboring gene microRNA 4517 Neighboring gene sphingolipid transporter 1 (putative)

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 Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Common variable immunodeficiency 2
MedGen: C3150354 OMIM: 240500 GeneReviews: Not available
Compare labs
Common variable immunodeficiency 3
MedGen: C3150738 OMIM: 613493 GeneReviews: Not available
Compare labs
Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci.
GeneReviews: Not available

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
matrix gag HIV-1 MA increases phosphorylation and the DNA-binding activity of CREB and c-Myc through activation of the cAMP/PKA and MEK/ERK signaling pathways. Both signaling pathways are synergistically activated upon co-stimulation through the CD19 receptor PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC12802

Gene Ontology Provided by GOA

General protein information

Preferred Names
B-lymphocyte antigen CD19
Names
B-lymphocyte surface antigen B4
T-cell surface antigen Leu-12
differentiation antigen CD19

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_007275.1 RefSeqGene

    Range
    5001..12409
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_35

mRNA and Protein(s)

  1. NM_001178098.2NP_001171569.1  B-lymphocyte antigen CD19 isoform 1 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AK313577, BC006338
    Consensus CDS
    CCDS53998.1
    UniProtKB/Swiss-Prot
    P15391
    Related
    ENSP00000313419.4, ENST00000324662.8
    Conserved Domains (2) summary
    smart00410
    Location:23115
    IG_like; Immunoglobulin like
    cl11960
    Location:22115
    Ig; Immunoglobulin domain
  2. NM_001385732.1NP_001372661.1  B-lymphocyte antigen CD19 isoform 3 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an alternate in-frame exon in the 5' coding region and uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. This results in a shorter protein (isoform 3) which lacks the first of two N-terminal Ig-like domains, compared to isoform 1.
    Source sequence(s)
    AC109460
    Conserved Domains (1) summary
    cd04979
    Location:93197
    Ig_Semaphorin_C; Immunoglobulin (Ig)-like domain at the C-terminus of semaphorins
  3. NM_001770.6NP_001761.3  B-lymphocyte antigen CD19 isoform 2 precursor

    See identical proteins and their annotated locations for NP_001761.3

    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 1.
    Source sequence(s)
    BC006338
    Consensus CDS
    CCDS10644.1
    UniProtKB/Swiss-Prot
    P15391
    Related
    ENSP00000437940.2, ENST00000538922.8
    Conserved Domains (2) summary
    smart00410
    Location:185274
    IG_like; Immunoglobulin like
    cl11960
    Location:22116
    Ig; Immunoglobulin domain

RNA

  1. NR_169755.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) retains an intron and uses an alternate splice site in the 5' end, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC109460
    Related
    ENST00000565089.5

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p13 Primary Assembly

    Range
    28931735..28939347
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006721103.3XP_006721166.1  B-lymphocyte antigen CD19 isoform X1

    Conserved Domains (2) summary
    smart00410
    Location:96185
    IG_like; Immunoglobulin like
    cl11960
    Location:99173
    Ig; Immunoglobulin domain
  2. XM_011545981.2XP_011544283.1  B-lymphocyte antigen CD19 isoform X3

    Conserved Domains (2) summary
    smart00410
    Location:23115
    IG_like; Immunoglobulin like
    cl11960
    Location:22115
    Ig; Immunoglobulin domain

RNA

  1. XR_950871.2 RNA Sequence

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