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LRRN3 leucine rich repeat neuronal 3 [ Homo sapiens (human) ]

Gene ID: 54674, updated on 5-Mar-2024

Summary

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Official Symbol
LRRN3provided by HGNC
Official Full Name
leucine rich repeat neuronal 3provided by HGNC
Primary source
HGNC:HGNC:17200
See related
Ensembl:ENSG00000173114 MIM:619748; AllianceGenome:HGNC:17200
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
NLRR3; NLRR-3; FIGLER5
Summary
Predicted to act upstream of or within positive regulation of synapse assembly. Predicted to be integral component of membrane. Predicted to be active in extracellular matrix and extracellular space. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in adrenal (RPKM 13.7), brain (RPKM 11.9) and 12 other tissues See more
Orthologs
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Genomic context

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Location:
7q31.1
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (111091127..111125454)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (112409397..112443727)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (110731183..110765510)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901723 Neighboring gene Sharpr-MPRA regulatory region 11752 Neighboring gene NANOG hESC enhancer GRCh37_chr7:110230392-110230942 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr7:110358473-110359258 Neighboring gene uncharacterized LOC124901724 Neighboring gene inner mitochondrial membrane peptidase subunit 2 Neighboring gene NANOG hESC enhancer GRCh37_chr7:110444579-110445080 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:110490168-110490726 Neighboring gene Sharpr-MPRA regulatory region 15683 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:110691790-110692442 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:110736847-110737774 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26505 Neighboring gene uncharacterized LOC124901853 Neighboring gene MPRA-validated peak6687 silencer Neighboring gene uncharacterized LOC124901725 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:110832884-110833522 Neighboring gene MPRA-validated peak6688 silencer Neighboring gene uncharacterized LOC124900232

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. Intracellular fragment of NLRR3 (NLRR3-ICD) stimulates ATRA-dependent neuroblastoma differentiation. Akter J, et al. Biochem Biophys Res Commun, 2014 Oct 10. PMID 25256744
  2. Expression of NLRR3 orphan receptor gene is negatively regulated by MYCN and Miz-1, and its downregulation is associated with unfavorable outcome in neuroblastoma. Akter J, et al. Clin Cancer Res, 2011 Nov 1. PMID 21908575
  3. Rat neuronal leucine-rich repeat protein-3: cloning and regulation of the gene expression. Fukamachi K, et al. Biochem Biophys Res Commun, 2001 Sep 14. PMID 11549284
  4. Polymorphisms in leucine-rich repeat genes are associated with autism spectrum disorder susceptibility in populations of European ancestry. Sousa I, et al. Mol Autism, 2010 Mar 25. PMID 20678249, Free PMC Article
  5. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. Clark HF, et al. Genome Res, 2003 Oct. PMID 12975309, Free PMC Article

See all (14) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. NLRR3 is proteolytically processed by secretases and its intracellular domain is then released to translocate into the cell nucleus during ATRA-mediated neuroblastoma differentiation.
    Title: Intracellular fragment of NLRR3 (NLRR3-ICD) stimulates ATRA-dependent neuroblastoma differentiation.
  2. NLRR3 is a direct target of MYCN, which associates with Miz-1 and negatively regulates NLRR3 expression. NLRR3 may play a role in NBL differentiation and the survival of NBL patients by inversely correlating with MYCN amplification.
    Title: Expression of NLRR3 orphan receptor gene is negatively regulated by MYCN and Miz-1, and its downregulation is associated with unfavorable outcome in neuroblastoma.
  3. Observational study of gene-disease association. (HuGE Navigator)
    Title: Polymorphisms in leucine-rich repeat genes are associated with autism spectrum disorder susceptibility in populations of European ancestry.
  4. 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)

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

  • FLJ11129

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in positive regulation of synapse assembly IEA
Inferred from Electronic Annotation
more info
  
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
  
located_in membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
leucine-rich repeat neuronal protein 3
Names
fibronectin type III, immunoglobulin and leucine rich repeat domains 5
leucine-rich repeat protein, neuronal 3
neuronal leucine-rich repeat protein 3

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_001099658.2 → NP_001093128.1  leucine-rich repeat neuronal protein 3 precursor

    See identical proteins and their annotated locations for NP_001093128.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2 and 3 encode the same protein.
    Source sequence(s)
    AL442092, AY358280, BC035133, DA494543
    Consensus CDS
    CCDS5754.1
    UniProtKB/Swiss-Prot
    O43377, Q6I9V8, Q8IYQ6, Q9H3W5
    UniProtKB/TrEMBL
    A4D0T1, A8K941
    Related
    ENSP00000312001.5, ENST00000308478.10
    Conserved Domains (6) summary
    TIGR00864
    Location:341 → 442
    PCC; polycystin cation channel protein
    smart00013
    Location:28 → 72
    LRRNT; Leucine rich repeat N-terminal domain
    COG4886
    Location:75 → 355
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00033
    Location:94 → 117
    LRR_RI; leucine-rich repeat [structural motif]
    pfam00041
    Location:526 → 593
    fn3; Fibronectin type III domain
    cl11960
    Location:437 → 513
    Ig; Immunoglobulin domain

  2. NM_001099660.2 → NP_001093130.1  leucine-rich repeat neuronal protein 3 precursor

    See identical proteins and their annotated locations for NP_001093130.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript. Variants 1, 2 and 3 encode the same protein.
    Source sequence(s)
    AK001991, AL442092, AY358280, BC035133, DA494543
    Consensus CDS
    CCDS5754.1
    UniProtKB/Swiss-Prot
    O43377, Q6I9V8, Q8IYQ6, Q9H3W5
    UniProtKB/TrEMBL
    A4D0T1, A8K941
    Related
    ENSP00000397312.1, ENST00000451085.5
    Conserved Domains (6) summary
    TIGR00864
    Location:341 → 442
    PCC; polycystin cation channel protein
    smart00013
    Location:28 → 72
    LRRNT; Leucine rich repeat N-terminal domain
    COG4886
    Location:75 → 355
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00033
    Location:94 → 117
    LRR_RI; leucine-rich repeat [structural motif]
    pfam00041
    Location:526 → 593
    fn3; Fibronectin type III domain
    cl11960
    Location:437 → 513
    Ig; Immunoglobulin domain

  3. NM_018334.5 → NP_060804.3  leucine-rich repeat neuronal protein 3 precursor

    See identical proteins and their annotated locations for NP_060804.3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2 and 3 encode the same protein.
    Source sequence(s)
    AF134481, AL442092, DA494543, DB095402
    Consensus CDS
    CCDS5754.1
    UniProtKB/Swiss-Prot
    O43377, Q6I9V8, Q8IYQ6, Q9H3W5
    UniProtKB/TrEMBL
    A4D0T1, A8K941
    Related
    ENSP00000412417.2, ENST00000422987.3
    Conserved Domains (6) summary
    TIGR00864
    Location:341 → 442
    PCC; polycystin cation channel protein
    smart00013
    Location:28 → 72
    LRRNT; Leucine rich repeat N-terminal domain
    COG4886
    Location:75 → 355
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00033
    Location:94 → 117
    LRR_RI; leucine-rich repeat [structural motif]
    pfam00041
    Location:526 → 593
    fn3; Fibronectin type III domain
    cl11960
    Location:437 → 513
    Ig; Immunoglobulin domain

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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    111091127..111125454
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    112409397..112443727
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9H3W5.1 GenPept UniProtKB/Swiss-Prot:Q9H3W5

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