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LRRC2 leucine rich repeat containing 2 [ Homo sapiens (human) ]

Gene ID: 79442, updated on 27-Nov-2024

Summary

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Official Symbol
LRRC2provided by HGNC
Official Full Name
leucine rich repeat containing 2provided by HGNC
Primary source
HGNC:HGNC:14676
See related
Ensembl:ENSG00000163827 MIM:607180; AllianceGenome:HGNC:14676
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
Summary
This gene encodes a member of the leucine-rich repeat-containing family of proteins, which function in diverse biological pathways. This family member may possibly be a nuclear protein. Similarity to the RAS suppressor protein, as well as expression down-regulation observed in tumor cells, suggests that it may function as a tumor suppressor. The gene is located in the chromosome 3 common eliminated region 1 (C3CER1), a 1.4 Mb region that is commonly deleted in diverse tumors. A related pseudogene has been identified on chromosome 2. [provided by RefSeq, Sep 2011]
Expression
Biased expression in heart (RPKM 15.6), thyroid (RPKM 11.1) and 9 other tissues See more
Orthologs
mouse all
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Genomic context

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See LRRC2 in Genome Data Viewer
Location:
3p21.31
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (46515385..46566302, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (46531490..46582384, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (46556875..46607792, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:46484307-46484808 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:46491889-46492388 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:46497203-46497704 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:46497705-46498204 Neighboring gene lactotransferrin Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:46511713-46512212 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:46519415-46519916 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:46519917-46520416 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:46530070-46530846 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:46530847-46531621 Neighboring gene Sharpr-MPRA regulatory region 6156 Neighboring gene receptor transporter protein 3 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr3:46561999-46563198 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19797 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:46585952-46586496 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:46598181-46598782 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:46604407-46604908 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:46605580-46606490 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:46606491-46607401 Neighboring gene LRRC2 antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 12028 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:46615492-46616264 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:46616265-46617037 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:46617811-46618582 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:46618583-46619356 Neighboring gene hESC enhancers GRCh37_chr3:46620129-46620901 and GRCh37_chr3:46620902-46621673 Neighboring gene cripto, EGF-CFC family member Neighboring gene NANOG hESC enhancer GRCh37_chr3:46646153-46646654 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:46659485-46659985 Neighboring gene family with sequence similarity 240 member A

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. Leucine-rich repeat (LRR) proteins: integrators of pattern recognition and signaling in immunity. Ng A, et al. Autophagy, 2011 Sep. PMID 21606681, Free PMC Article
  2. Identifying mRNA targets of microRNA dysregulated in cancer: with application to clear cell Renal Cell Carcinoma. Liu H, et al. BMC Syst Biol, 2010 Apr 27. PMID 20420713, Free PMC Article
  3. Down regulation of 3p genes, LTF, SLC38A3 and DRR1, upon growth of human chromosome 3-mouse fibrosarcoma hybrids in severe combined immunodeficiency mice. Kholodnyuk ID, et al. Int J Cancer, 2006 Jul 1. PMID 16432833
  4. Human leucine-rich repeat proteins: a genome-wide bioinformatic categorization and functional analysis in innate immunity. Ng AC, et al. Proc Natl Acad Sci U S A, 2011 Mar 15. PMID 20616063, Free PMC Article
  5. The transcriptional map of the common eliminated region 1 (C3CER1) in 3p21.3. Kiss H, et al. Eur J Hum Genet, 2002 Jan. PMID 11896456

See all (16) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
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

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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Replication interactions

Interaction Pubs
Knockdown of leucine rich repeat containing 2 (LRRC2) by siRNA enhances the early stages of HIV-1 replication in HeLa-CD4 cells infected with viral pseudotypes HIV89.6R and HIV8.2N 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

Homology

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in intracellular signal transduction IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
leucine-rich repeat-containing protein 2

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_021214.1 RefSeqGene

    Range
    18781..69698
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_024512.5 → NP_078788.2  leucine-rich repeat-containing protein 2

    See identical proteins and their annotated locations for NP_078788.2

    Status: REVIEWED

    Source sequence(s)
    AC098613, AJ308569, AK057808, BP420656
    Consensus CDS
    CCDS2741.1
    UniProtKB/Swiss-Prot
    B2RDQ7, Q96LT5, Q9BYS8
    UniProtKB/TrEMBL
    B2RBH0, Q53F49
    Related
    ENSP00000379241.3, ENST00000395905.8
    Conserved Domains (3) summary
    sd00033
    Location:123 → 145
    LRR_RI; leucine-rich repeat [structural motif]
    pfam12799
    Location:167 → 201
    LRR_4; Leucine Rich repeats (2 copies)
    pfam13855
    Location:237 → 295
    LRR_8; Leucine rich repeat

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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    46515385..46566302 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    46531490..46582384 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_024750.3: Suppressed sequence

    Description
    NM_024750.3: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate due to the presence of an upstream ORF with a strong Kozak signal.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9BYS8.2 GenPept UniProtKB/Swiss-Prot:Q9BYS8

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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