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LRRC3B leucine rich repeat containing 3B [ Homo sapiens (human) ]

Gene ID: 116135, updated on 11-Apr-2024

Summary

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Official Symbol
LRRC3Bprovided by HGNC
Official Full Name
leucine rich repeat containing 3Bprovided by HGNC
Primary source
HGNC:HGNC:28105
See related
Ensembl:ENSG00000179796 MIM:618996; AllianceGenome:HGNC:28105
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
LRP15
Summary
The protein encoded by this gene is a tumor suppressor, with lowered expression levels found in gastric, renal, colorectal, lung, and breast cancer tissues. The promoter of this gene is frequently hypermethylated in these cancer tissues, although the hypermethylation does not appear to be the cause of the reduced expression of this gene. Several transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Dec 2015]
Expression
Biased expression in brain (RPKM 1.4), testis (RPKM 0.6) and 3 other tissues See more
Orthologs
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Genomic context

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Location:
3p24.1
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (26622772..26710776)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (26625372..26713383)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (26664263..26752267)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 9567 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:26431392-26431996 Neighboring gene VENT homeobox pseudogene 4 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:26478985-26480184 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:26663597-26664112 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:26665705-26666674 Neighboring gene LRRC3B antisense RNA 1 Neighboring gene uncharacterized LOC124909488 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:26727688-26727896 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:26824878-26825470 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:26824284-26824877 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19615 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:27083978-27084542 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:27084543-27085106 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:27085107-27085671 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr3:27141697-27142896 Neighboring gene NANOG hESC enhancer GRCh37_chr3:27147157-27147736 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14148 Neighboring gene NIMA related kinase 10 Neighboring gene MPRA-validated peak4579 silencer Neighboring gene MICOS10 pseudogene 3 Neighboring gene RNA, U6 small nuclear 342, pseudogene

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. LRRC3B and its promoter hypomethylation status predicts response to anti-PD-1 based immunotherapy. Luo L, et al. Front Immunol, 2023. PMID 36798137, Free PMC Article
  2. [LRRC3B is Downregulated in Non-small Cell Lung Cancer and Connected with Cell Proliferation and Invasion]. Kan L, et al. Zhongguo Fei Ai Za Zhi, 2016 Apr 20. PMID 27118644, Free PMC Article
  3. LRRC3B is downregulated in non-small-cell lung cancer and inhibits cancer cell proliferation and invasion. Kan L, et al. Tumour Biol, 2016 Jan. PMID 26276358
  4. The clinical value of LRRC3B gene expression and promoter hypermethylation in breast carcinomas. Wang Y, et al. Cell Biochem Biophys, 2014 Nov. PMID 24839112
  5. LRRC3B gene is frequently epigenetically inactivated in several epithelial malignancies and inhibits cell growth and replication. Haraldson K, et al. Biochimie, 2012 May. PMID 22321817

See all (21) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. LRRC3B and its promoter hypomethylation status predicts response to anti-PD-1 based immunotherapy.
    Title: LRRC3B and its promoter hypomethylation status predicts response to anti-PD-1 based immunotherapy.
  2. The expression of LRRC3B is downregulated in non-small cell lung cancer compared with normal epithelial cells.
    Title: [LRRC3B is Downregulated in Non-small Cell Lung Cancer and Connected with Cell Proliferation and Invasion].
  3. LRRC3B may serve as an important tumor suppressor in non-small-cell lung cancer
    Title: LRRC3B is downregulated in non-small-cell lung cancer and inhibits cancer cell proliferation and invasion.
  4. LRRC3B gene expression and promoter hypermethylation in breast carcinomas
    Title: The clinical value of LRRC3B gene expression and promoter hypermethylation in breast carcinomas.
  5. Data suggest that LRRC3B gene could be involved in the process of carcinogenesis as a tumor suppressor gene.
    Title: LRRC3B gene is frequently epigenetically inactivated in several epithelial malignancies and inhibits cell growth and replication.
  6. The LRRC3B gene promoter was methylated in 43% of clear cell renal carcinoma samples.
    Title: Methylation pattern of the putative tumor-suppressor gene LRRC3B promoter in clear cell renal cell carcinomas.
  7. LRRC3B may be a novel methylation-sensitive tumor suppressor gene in CRC. LRRC3B methylation has significant tumor specificity and may be a biomarker of CRC.
    Title: Epigenetic silencing of LRRC3B in colorectal cancer.
  8. suggest that LRRC3B is a putative tumor suppressor gene that is silenced in gastric cancers by epigenetic mechanisms and that LRRC3B silencing in cancer may play an important role in tumor escape from immune surveillance
    Title: LRRC3B, encoding a leucine-rich repeat-containing protein, is a putative tumor suppressor gene in gastric cancer.
  9. The expression of LRP15 is controlled by methylation in its promoter in HeLa cells, and LRP15 confers resistance to ultraviolet rays damage and accelerates the DNA repair rate.
    Title: The novel gene LRP15 is regulated by DNA methylation and confers increased efficiency of DNA repair of ultraviolet-induced DNA damage.
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)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC102927, AC114877.3

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Component Evidence Code Pubs
is_active_in extracellular matrix IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
leucine-rich repeat-containing protein 3B
Names
leucine-rich repeat protein 15
leucine-rich repeat protein LRP15

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.

mRNA and Protein(s)

  1. NM_001317808.2 → NP_001304737.1  leucine-rich repeat-containing protein 3B precursor

    Status: REVIEWED

    Source sequence(s)
    AC099754, AC114877, BC040656, DA414440
    Consensus CDS
    CCDS2644.1
    UniProtKB/Swiss-Prot
    Q5M8T0, Q96PB8
    Conserved Domains (3) summary
    smart00013
    Location:33 → 68
    LRRNT; Leucine rich repeat N-terminal domain
    sd00031
    Location:66 → 89
    LRR_1; leucine-rich repeat [structural motif]
    pfam13855
    Location:69 → 125
    LRR_8; Leucine rich repeat

  2. NM_001317809.2 → NP_001304738.1  leucine-rich repeat-containing protein 3B precursor

    Status: REVIEWED

    Source sequence(s)
    AC099754, BC040656, BC067784, BI917966
    Consensus CDS
    CCDS2644.1
    UniProtKB/Swiss-Prot
    Q5M8T0, Q96PB8
    Conserved Domains (3) summary
    smart00013
    Location:33 → 68
    LRRNT; Leucine rich repeat N-terminal domain
    sd00031
    Location:66 → 89
    LRR_1; leucine-rich repeat [structural motif]
    pfam13855
    Location:69 → 125
    LRR_8; Leucine rich repeat

  3. NM_001317810.3 → NP_001304739.1  leucine-rich repeat-containing protein 3B precursor

    Status: REVIEWED

    Source sequence(s)
    AC099754, AC114877
    Consensus CDS
    CCDS2644.1
    UniProtKB/Swiss-Prot
    Q5M8T0, Q96PB8
    Related
    ENSP00000406370.1, ENST00000417744.5
    Conserved Domains (3) summary
    smart00013
    Location:33 → 68
    LRRNT; Leucine rich repeat N-terminal domain
    sd00031
    Location:66 → 89
    LRR_1; leucine-rich repeat [structural motif]
    pfam13855
    Location:69 → 125
    LRR_8; Leucine rich repeat

  4. NM_001317811.2 → NP_001304740.1  leucine-rich repeat-containing protein 3B precursor

    Status: REVIEWED

    Source sequence(s)
    AC099754, BC087849
    Consensus CDS
    CCDS2644.1
    UniProtKB/Swiss-Prot
    Q5M8T0, Q96PB8
    Related
    ENSP00000394940.2, ENST00000456208.2
    Conserved Domains (3) summary
    smart00013
    Location:33 → 68
    LRRNT; Leucine rich repeat N-terminal domain
    sd00031
    Location:66 → 89
    LRR_1; leucine-rich repeat [structural motif]
    pfam13855
    Location:69 → 125
    LRR_8; Leucine rich repeat

  5. NM_001395645.1 → NP_001382574.1  leucine-rich repeat-containing protein 3B precursor

    Status: REVIEWED

    Source sequence(s)
    AC099754, AC114877
    Consensus CDS
    CCDS2644.1
    UniProtKB/Swiss-Prot
    Q5M8T0, Q96PB8
    Conserved Domains (3) summary
    smart00013
    Location:33 → 68
    LRRNT; Leucine rich repeat N-terminal domain
    sd00031
    Location:66 → 89
    LRR_1; leucine-rich repeat [structural motif]
    pfam13855
    Location:69 → 125
    LRR_8; Leucine rich repeat

  6. NM_001395646.1 → NP_001382575.1  leucine-rich repeat-containing protein 3B precursor

    Status: REVIEWED

    Source sequence(s)
    AC099754, AC114877
    Consensus CDS
    CCDS2644.1
    UniProtKB/Swiss-Prot
    Q5M8T0, Q96PB8
    Related
    ENSP00000497471.1, ENST00000648296.1
    Conserved Domains (3) summary
    smart00013
    Location:33 → 68
    LRRNT; Leucine rich repeat N-terminal domain
    sd00031
    Location:66 → 89
    LRR_1; leucine-rich repeat [structural motif]
    pfam13855
    Location:69 → 125
    LRR_8; Leucine rich repeat

  7. NM_001395647.1 → NP_001382576.1  leucine-rich repeat-containing protein 3B precursor

    Status: REVIEWED

    Source sequence(s)
    AC099754, AC114877
    Consensus CDS
    CCDS2644.1
    UniProtKB/Swiss-Prot
    Q5M8T0, Q96PB8
    Conserved Domains (3) summary
    smart00013
    Location:33 → 68
    LRRNT; Leucine rich repeat N-terminal domain
    sd00031
    Location:66 → 89
    LRR_1; leucine-rich repeat [structural motif]
    pfam13855
    Location:69 → 125
    LRR_8; Leucine rich repeat

  8. NM_052953.4 → NP_443185.1  leucine-rich repeat-containing protein 3B precursor

    See identical proteins and their annotated locations for NP_443185.1

    Status: REVIEWED

    Source sequence(s)
    AC099754, BC040656, BC067784
    Consensus CDS
    CCDS2644.1
    UniProtKB/Swiss-Prot
    Q5M8T0, Q96PB8
    Related
    ENSP00000379880.2, ENST00000396641.7
    Conserved Domains (3) summary
    smart00013
    Location:33 → 68
    LRRNT; Leucine rich repeat N-terminal domain
    sd00031
    Location:66 → 89
    LRR_1; leucine-rich repeat [structural motif]
    pfam13855
    Location:69 → 125
    LRR_8; Leucine rich repeat

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

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    26622772..26710776
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011533332.4 → XP_011531634.1  leucine-rich repeat-containing protein 3B isoform X1

    See identical proteins and their annotated locations for XP_011531634.1

    UniProtKB/Swiss-Prot
    Q5M8T0, Q96PB8
    Conserved Domains (3) summary
    smart00013
    Location:33 → 68
    LRRNT; Leucine rich repeat N-terminal domain
    sd00031
    Location:66 → 89
    LRR_1; leucine-rich repeat [structural motif]
    pfam13855
    Location:69 → 125
    LRR_8; Leucine rich repeat

  2. XM_047447402.1 → XP_047303358.1  leucine-rich repeat-containing protein 3B isoform X1

    UniProtKB/Swiss-Prot
    Q5M8T0, Q96PB8

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    26625372..26713383
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054345141.1 → XP_054201116.1  leucine-rich repeat-containing protein 3B isoform X1

    UniProtKB/Swiss-Prot
    Q5M8T0, Q96PB8

  2. XM_054345140.1 → XP_054201115.1  leucine-rich repeat-containing protein 3B isoform X1

    UniProtKB/Swiss-Prot
    Q5M8T0, Q96PB8
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96PB8.1 GenPept UniProtKB/Swiss-Prot:Q96PB8

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