VPREB1 V-set pre-B cell surrogate light chain 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: VPREB1provided by HGNC
Official Full Name: V-set pre-B cell surrogate light chain 1provided by HGNC
Primary source: HGNC:HGNC:12709
See related: Ensembl:ENSG00000169575 IMGT/GENE-DB:VPREB1; MIM:605141; AllianceGenome:HGNC:12709
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: IGI; IGVPB; VPREB; CD179a
Summary: The protein encoded by this gene belongs to the immunoglobulin superfamily and is expressed selectively at the early stages of B cell development, namely, in proB and early preB cells. This gene encodes the iota polypeptide chain that is associated with the Ig-mu chain to form a molecular complex which is expressed on the surface of pre-B cells. The complex is thought to regulate Ig gene rearrangements in the early steps of B-cell differentiation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2015]
Orthologs: mouse all
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Genomic context

Location:: 22q11.22

Exon count:: 2

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	22	NC_000022.11 (22244786..22245515)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	22	NC_060946.1 (22658325..22659054)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	22	NC_000022.10 (22599198..22599927)

Chromosome 22 - NC_000022.11 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?

Mutational Analysis of the VPREB1 Gene of Pre-BCR Complex in a Cohort of Sporadic Pediatric Patients With B-Cell Acute Lymphoblastic Leukemia.
Title: Mutational Analysis of the VPREB1 Gene of Pre-BCR Complex in a Cohort of Sporadic Pediatric Patients With B-Cell Acute Lymphoblastic Leukemia.
Association of VPREB1 Gene Copy Number Variation and Rheumatoid Arthritis Susceptibility.
Title: Association of VPREB1 Gene Copy Number Variation and Rheumatoid Arthritis Susceptibility.
CRISPR/Cas9 mediated knock-out of VPREB1 gene induces a cytotoxic effect in myeloma cells.
Title: CRISPR/Cas9 mediated knock-out of VPREB1 gene induces a cytotoxic effect in myeloma cells.
Irrespective of subtype, Acute Lymphoblastic Leukemia with high levels of IGHM, IGLL1 and VPREB1 are arrested at the pre-B stage and correlate with good prognosis in high-risk pediatric B-cell precursor acute lymphoblastic leukemia.
Title: The Expression Pattern of the Pre-B Cell Receptor Components Correlates with Cellular Stage and Clinical Outcome in Acute Lymphoblastic Leukemia.
VPREB1 focal deletions are common in B-ALL and occur independent of V(D)J light chain recombination. Focal deletions of VPREB1 correlate with decreased expression levels and high-risk patients with focal deletions tend to have poorer overall survival
Title: VPREB1 deletions occur independent of lambda light chain rearrangement in childhood acute lymphoblastic leukemia.
The proportion of the individuals with <2 copies of the VPREB1 gene was significantly higher in the patient group than that in the controls, while that of the individuals with >2 copies was lower in the patient group than that in the controls.
Title: The potential role of VPREB1 gene copy number variation in susceptibility to rheumatoid arthritis.
Observational study of gene-disease association. (HuGE Navigator)
Title: New genetic associations detected in a host response study to hepatitis B vaccine.
The 5' region of the VpreB gene contains a promoter which displays higher relative activity in preB cells compared with cells at other stages or from other lineages.
Title: The human V-preB promoter is a target for coordinated activation by early B cell factor and E47.
Pre-B cell integrins and their stromal cell ligands together with the pre-B cell receptor and galectin-1 form a homogeneous lattice at the contact area between bone marrow pre-B and stromal cells.
Title: Clustering of pre-B cell integrins induces galectin-1-dependent pre-B cell receptor relocalization and activation.

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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

EBI GWAS Catalog

Description
Genome-wide association study of chronic periodontitis in a general German population. 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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by GOA

Process	Evidence Code	Pubs
involved_in immune response	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in endoplasmic reticulum	IEA Inferred from Electronic Annotation more info
located_in extracellular region	TAS Traceable Author Statement more info
part_of immunoglobulin complex	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: immunoglobulin iota chain

Names: CD179 antigen-like family member A; pre-B lymphocyte 1; v(pre)B protein

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_029387.2 RefSeqGene

Range

4997..5726

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GenBank, FASTA, Sequence Viewer (Graphics)
NG_000002.1

Range

223181..223916

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001303509.2 → NP_001290438.1 immunoglobulin iota chain isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate splice site in the coding region and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) has a distinct N-terminus and is shorter than isoform 1.

Source sequence(s)

AC245060

Consensus CDS

CCDS77657.1

Conserved Domains (2) summary

cd00096
Location:36 → 40

Ig; Ig strand B [structural motif]

cl11960
Location:21 → 117

Ig; Immunoglobulin domain
NM_007128.4 → NP_009059.1 immunoglobulin iota chain isoform 1 precursor

See identical proteins and their annotated locations for NP_009059.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AC245060, BC017922, BG502270

Consensus CDS

CCDS13798.1

UniProtKB/Swiss-Prot

B5MCG2, P12018

Related

ENSP00000385361.3, ENST00000403807.4

Conserved Domains (2) summary

smart00410
Location:26 → 116

IG_like; Immunoglobulin like

cl11960
Location:30 → 118

Ig; Immunoglobulin domain