CD19 CD19 molecule [Homo sapiens (human)] - Gene

Summary

Official Symbol: CD19provided by HGNC
Official Full Name: CD19 moleculeprovided by HGNC
Primary source: HGNC:HGNC:1633
See related: Ensembl:ENSG00000177455 MIM:107265; AllianceGenome:HGNC:1633
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: mouse all
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Genomic context

Location:: 16p11.2

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	16	NC_000016.10 (28931971..28939342)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	16	NC_060940.1 (29213087..29220458)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	16	NC_000016.9 (28943292..28950663)

Chromosome 16 - NC_000016.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

Evaluation of transcription factors and cytokine expressions of T-cell subsets in CD19 deficiency and their possible relationship with autoimmune disease.
Title: Evaluation of transcription factors and cytokine expressions of T-cell subsets in CD19 deficiency and their possible relationship with autoimmune disease.
Novel chimeric antigen receptor targets and constructs for acute lymphoblastic leukemia: Moving beyond CD19.
Title: Novel chimeric antigen receptor targets and constructs for acute lymphoblastic leukemia: Moving beyond CD19.
CD19+ B cell values predict the increase of anti-SARS CoV2 antibodies in fingolimod-treated and COVID-19-vaccinated patients with multiple sclerosis.
Title: CD19+ B cell values predict the increase of anti-SARS CoV2 antibodies in fingolimod-treated and COVID-19-vaccinated patients with multiple sclerosis.
Transcriptional signatures associated with persisting CD19 CAR-T cells in children with leukemia.
Title: Transcriptional signatures associated with persisting CD19 CAR-T cells in children with leukemia.
Compromised antigen binding and signaling interfere with bispecific CD19 and CD79a chimeric antigen receptor function.
Title: Compromised antigen binding and signaling interfere with bispecific CD19 and CD79a chimeric antigen receptor function.
Host B cells escape CAR-T immunotherapy by reversible downregulation of CD19.
Title: Host B cells escape CAR-T immunotherapy by reversible downregulation of CD19.
NUDT21 limits CD19 levels through alternative mRNA polyadenylation in B cell acute lymphoblastic leukemia.
Title: NUDT21 limits CD19 levels through alternative mRNA polyadenylation in B cell acute lymphoblastic leukemia.
B-lineage antigens that are useful to substitute CD19 for minimal residual disease monitoring in B cell precursor acute lymphoblastic leukemia after CD19 targeting.
Title: B-lineage antigens that are useful to substitute CD19 for minimal residual disease monitoring in B cell precursor acute lymphoblastic leukemia after CD19 targeting.
Identification of genomic signatures in bone marrow associated with clinical response of CD19 CAR T-cell therapy.
Title: Identification of genomic signatures in bone marrow associated with clinical response of CD19 CAR T-cell therapy.
CD19 target evasion as a mechanism of relapse in large B-cell lymphoma treated with axicabtagene ciloleucel.
Title: CD19 target evasion as a mechanism of relapse in large B-cell lymphoma treated with axicabtagene ciloleucel.

Submit: New GeneRIF Correction See all GeneRIFs (117)

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
Immunodeficiency, common variable, 2 MedGen: C3150354 OMIM: 240500 GeneReviews: Not available	Compare labs
Immunodeficiency, common variable, 3 MedGen: C3150738 OMIM: 613493 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci. 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)

HIV-1 interactions

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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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH65240 (e-PCR)
- UniSTS:87340

PMC136845P2 (e-PCR)
- UniSTS:270805

GDB:191081 (e-PCR)
- UniSTS:155642

G10610 (e-PCR)
- UniSTS:23292

Gene Ontology Provided by GOA

Process	Evidence Code	Pubs
involved_in B cell proliferation involved in immune response	IDA Inferred from Direct Assay more info	PubMed
involved_in B cell proliferation involved in immune response	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in B cell receptor signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in B cell receptor signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in B-1 B cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in antigen receptor-mediated signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in immunoglobulin mediated immune response	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of release of sequestered calcium ion into cytosol	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of release of sequestered calcium ion into cytosol	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of B cell activation	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of B cell receptor signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in external side of plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in external side of plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in extracellular exosome	HDA more info	PubMed
located_in membrane raft	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	TAS Traceable Author Statement more info
part_of protein-containing complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

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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

NG_007275.1 RefSeqGene

Range

5001..12409

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_35

mRNA and Protein(s)

NM_001178098.2 → NP_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/TrEMBL

B4DVP4

Related

ENSP00000313419.4, ENST00000324662.8

Conserved Domains (2) summary

smart00410
Location:23 → 115

IG_like; Immunoglobulin like

cl11960
Location:22 → 115

Ig; Immunoglobulin domain
NM_001385732.1 → NP_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

UniProtKB/TrEMBL

B4E2W1

Conserved Domains (1) summary

cd04979
Location:93 → 197

Ig_Semaphorin_C; Immunoglobulin (Ig)-like domain at the C-terminus of semaphorins
NM_001770.6 → NP_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

A0N0P9, F5H635, P15391, Q96S68, Q9BRD6

UniProtKB/TrEMBL

B4DVP4

Related

ENSP00000437940.2, ENST00000538922.8

Conserved Domains (2) summary

smart00410
Location:185 → 274

IG_like; Immunoglobulin like

cl11960
Location:22 → 116

Ig; Immunoglobulin domain

RNA

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: 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_000016.10 Reference GRCh38.p14 Primary Assembly

Range

28931971..28939342

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011545981.3 → XP_011544283.1 B-lymphocyte antigen CD19 isoform X1

Conserved Domains (2) summary

smart00410
Location:23 → 115

IG_like; Immunoglobulin like

cl11960
Location:22 → 115

Ig; Immunoglobulin domain