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LRFN4 leucine rich repeat and fibronectin type III domain containing 4 [ Homo sapiens (human) ]

Gene ID: 78999, updated on 11-Apr-2024

Summary

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Official Symbol
LRFN4provided by HGNC
Official Full Name
leucine rich repeat and fibronectin type III domain containing 4provided by HGNC
Primary source
HGNC:HGNC:28456
See related
Ensembl:ENSG00000173621 MIM:612810; AllianceGenome:HGNC:28456
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
SALM3; SALM3.; FIGLER6
Summary
Predicted to be involved in regulation of postsynaptic density assembly; regulation of presynapse assembly; and synaptic membrane adhesion. Predicted to be located in plasma membrane. Predicted to be active in GABA-ergic synapse; cell surface; and glutamatergic synapse. Predicted to be integral component of postsynaptic density membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in fat (RPKM 5.8), colon (RPKM 4.2) and 22 other tissues See more
Orthologs
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Genomic context

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Location:
11q13.2
Exon count:
3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (66857064..66860475)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (66853340..66856751)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (66624535..66627946)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene TOP6B like initiator of meiotic double strand breaks Neighboring gene ferritin light chain pseudogene 6 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:66580049-66580832 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:66609109-66609235 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3603 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:66610783-66611489 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:66617715-66618294 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:66618295-66618873 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3605 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3606 Neighboring gene Ras converting CAAX endopeptidase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5058 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:66644024-66644524 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:66644525-66645025 Neighboring gene pyruvate carboxylase Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:66645752-66646490 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:66649447-66650184 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:66650185-66650922 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5059 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:66672605-66673252 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5060 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:66688620-66689560 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:66690541-66691041 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:66691815-66692466 Neighboring gene RNA, U7 small nuclear 23 pseudogene Neighboring gene microRNA 3163

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. [Expression and clinical significance of LRFN4 in colorectal cancer tissue]. Zheng F, et al. Zhonghua Yi Xue Za Zhi, 2020 Jun 9. PMID 32536098
  2. High SALM3 Expression in Tumor Cells and Fibroblasts Is Correlated with Poor Prognosis in Gastric Cancer Patients. Liu Y, et al. Dis Markers, 2019. PMID 31089399, Free PMC Article
  3. A neuronal transmembrane protein LRFN4 induces monocyte/macrophage migration via actin cytoskeleton reorganization. Konakahara S, et al. FEBS Lett, 2011 Jul 21. PMID 21704618
  4. Splicing-Dependent Trans-synaptic SALM3-LAR-RPTP Interactions Regulate Excitatory Synapse Development and Locomotion. Li Y, et al. Cell Rep, 2015 Sep 8. PMID 26321637, Free PMC Article
  5. A neuronal transmembrane protein LRFN4 complexes with 14-3-3s and NCK1 to induce morphological change in monocytic cells via Rac1-mediated actin cytoskeleton reorganization. Konakahara S, et al. FEBS Lett, 2012 Jul 30. PMID 22677168

See all (23) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. [Expression and clinical significance of LRFN4 in colorectal cancer tissue].
    Title: [Expression and clinical significance of LRFN4 in colorectal cancer tissue].
  2. SALM3 is overexpressed in the tumor cells and fibroblasts of gastric cancer patients. High SALM3 expression is associated with poor prognosis.
    Title: High SALM3 Expression in Tumor Cells and Fibroblasts Is Correlated with Poor Prognosis in Gastric Cancer Patients.
  3. SALM3 regulates excitatory synapse development and locomotion behavior.
    Title: Splicing-Dependent Trans-synaptic SALM3-LAR-RPTP Interactions Regulate Excitatory Synapse Development and Locomotion.
  4. LRFN4 complexed with 14-3-3s and NCK1 to mediate elongation in monocytic cells via Rac-1-mediated actin cytoskeleton reorganization
    Title: A neuronal transmembrane protein LRFN4 complexes with 14-3-3s and NCK1 to induce morphological change in monocytic cells via Rac1-mediated actin cytoskeleton reorganization.
  5. Data indicate that LRFN4 signaling plays an important role in the migration of monocytes/macrophages.
    Title: A neuronal transmembrane protein LRFN4 induces monocyte/macrophage migration via actin cytoskeleton reorganization.
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

EBI GWAS Catalog

Description
Large-scale genome-wide association analysis of bipolar disorder identifies a new susceptibility locus near ODZ4.
EBI GWAS Catalog

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

HIV-1 interactions

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Replication interactions

Interaction Pubs
HIV-1 infection (VSV-G pseudotyped) of CEMT4 T cells downregulates plasma membrane expression of LRFN4 PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC3103

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in regulation of postsynaptic density assembly IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of presynapse assembly IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in synaptic membrane adhesion IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in GABA-ergic synapse IEA
Inferred from Electronic Annotation
more info
  
is_active_in cell surface IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in glutamatergic synapse IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in plasma membrane TAS
Traceable Author Statement
more info
  
is_active_in postsynaptic density membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in postsynaptic density membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
leucine-rich repeat and fibronectin type-III domain-containing protein 4
Names
fibronectin type III, immunoglobulin and leucine rich repeat domains 6

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_001363524.2 → NP_001350453.1  leucine-rich repeat and fibronectin type-III domain-containing protein 4 precursor

    Status: VALIDATED

    Source sequence(s)
    AP003176
    Consensus CDS
    CCDS8153.1
    UniProtKB/Swiss-Prot
    Q4VBZ3, Q59GV4, Q6PJG9, Q8N644, Q9BWJ0
    Conserved Domains (5) summary
    cd05764
    Location:295 → 368
    Ig_2; Subgroup of the immunoglobulin (Ig) superfamily
    smart00082
    Location:234 → 278
    LRRCT; Leucine rich repeat C-terminal domain
    sd00033
    Location:50 → 73
    LRR_RI; leucine-rich repeat [structural motif]
    pfam00041
    Location:409 → 478
    fn3; Fibronectin type III domain
    pfam13855
    Location:97 → 157
    LRR_8; Leucine rich repeat

  2. NM_024036.5 → NP_076941.2  leucine-rich repeat and fibronectin type-III domain-containing protein 4 precursor

    See identical proteins and their annotated locations for NP_076941.2

    Status: VALIDATED

    Source sequence(s)
    AP003176, BC015581, CN297399
    Consensus CDS
    CCDS8153.1
    UniProtKB/Swiss-Prot
    Q4VBZ3, Q59GV4, Q6PJG9, Q8N644, Q9BWJ0
    Related
    ENSP00000312535.4, ENST00000309602.5
    Conserved Domains (5) summary
    cd05764
    Location:295 → 368
    Ig_2; Subgroup of the immunoglobulin (Ig) superfamily
    smart00082
    Location:234 → 278
    LRRCT; Leucine rich repeat C-terminal domain
    sd00033
    Location:50 → 73
    LRR_RI; leucine-rich repeat [structural motif]
    pfam00041
    Location:409 → 478
    fn3; Fibronectin type III domain
    pfam13855
    Location:97 → 157
    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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    66857064..66860475
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    66853340..66856751
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q6PJG9.1 GenPept UniProtKB/Swiss-Prot:Q6PJG9

Gene LinkOut

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

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