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    LRFN5 leucine rich repeat and fibronectin type III domain containing 5 [ Homo sapiens (human) ]

    Gene ID: 145581, updated on 10-Dec-2024

    Summary

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    Official Symbol
    LRFN5provided by HGNC
    Official Full Name
    leucine rich repeat and fibronectin type III domain containing 5provided by HGNC
    Primary source
    HGNC:HGNC:20360
    See related
    Ensembl:ENSG00000165379 MIM:612811; AllianceGenome:HGNC:20360
    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
    SALM5; FIGLER8; C14orf146
    Summary
    This gene encodes a protein that belongs to the leucine-rich repeat and fibronectin type III domain-containing family of proteins. A similar protein in mouse, a glycosylated transmembrane protein, is thought to function in presynaptic differentiation. [provided by RefSeq, Sep 2016]
    Expression
    Biased expression in brain (RPKM 2.4), adrenal (RPKM 0.8) and 13 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See LRFN5 in Genome Data Viewer
    Location:
    14q21.1
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (41606876..41904549)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (35797646..36095321)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (42076079..42373752)

    Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA SNORA31 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr14:42068185-42068934 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr14:42068935-42069684 Neighboring gene LRFN5 divergent transcript Neighboring gene FKBP prolyl isomerase 1B pseudogene 1 Neighboring gene uncharacterized LOC124903305 Neighboring gene olfactory receptor family 10 subfamily V member 7 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. LRFN5 locus structure is associated with autism and influenced by the sex of the individual and locus conversions. Lybaek H, et al. Autism Res, 2022 Mar. PMID 35088940, Free PMC Article
    2. Identification of novel common variants associated with chronic pain using conditional false discovery rate analysis with major depressive disorder and assessment of pleiotropic effects of LRFN5. Johnston KJA, et al. Transl Psychiatry, 2019 Nov 20. PMID 31748543, Free PMC Article
    3. Microdeletion of pseudogene chr14.232.a affects LRFN5 expression in cells of a patient with autism spectrum disorder. Cappuccio G, et al. Eur J Hum Genet, 2019 Sep. PMID 31152157, Free PMC Article
    4. Structural basis of SALM5-induced PTPδ dimerization for synaptic differentiation. Lin Z, et al. Nat Commun, 2018 Jan 18. PMID 29348579, Free PMC Article
    5. Structural basis of trans-synaptic interactions between PTPδ and SALMs for inducing synapse formation. Goto-Ito S, et al. Nat Commun, 2018 Jan 18. PMID 29348429, Free PMC Article

    See all (20) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. LRFN5 and OLFM4 as novel potential biomarkers for major depressive disorder: a pilot study.
      Title: LRFN5 and OLFM4 as novel potential biomarkers for major depressive disorder: a pilot study.
    2. CircLRFN5 inhibits the progression of glioblastoma via PRRX2/GCH1 mediated ferroptosis.
      Title: CircLRFN5 inhibits the progression of glioblastoma via PRRX2/GCH1 mediated ferroptosis.
    3. LRFN5 locus structure is associated with autism and influenced by the sex of the individual and locus conversions.
      Title: LRFN5 locus structure is associated with autism and influenced by the sex of the individual and locus conversions.
    4. Identification of novel common variants associated with chronic pain using conditional false discovery rate analysis with major depressive disorder and assessment of pleiotropic effects of LRFN5.
      Title: Identification of novel common variants associated with chronic pain using conditional false discovery rate analysis with major depressive disorder and assessment of pleiotropic effects of LRFN5.
    5. we found that chr14.232.a increases expression of LRFN5 in his fibroblasts. Reduced expression of LRFN5 in fibroblasts should be interpreted with caution as these cells might not be representative of expression in brain cells, which are involved in the neurodevelopmental phenotype.
      Title: Microdeletion of pseudogene chr14.232.a affects LRFN5 expression in cells of a patient with autism spectrum disorder.
    6. Presynaptic differentiation induced by protein tyrosine phosphatase receptor type D (PTPdelta)-leucine rich repeat and fibronectin type III domain containing 5 (SALM5) requires the dimeric property of SALM5.
      Title: Structural basis of trans-synaptic interactions between PTPδ and SALMs for inducing synapse formation.
    7. In the 2:2 heterotetrameric SALM5/PTPdelta complex, a SALM5 dimer bridges two separate PTPdelta molecules.
      Title: Structural basis of SALM5-induced PTPδ dimerization for synaptic differentiation.
    8. SALM5/Lrfn5, has recently been implicated in severe progressive autism and familial schizophrenia, pointing to the clinical importance of SALMs.[review]
      Title: The SALM/Lrfn family of leucine-rich repeat-containing cell adhesion molecules.
    9. 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.
    10. Expression of SALM family proteins SALM3 and SALM5 in nonneural and neural cells induces both excitatory and inhibitory presynaptic differentiation in contacting axons.
      Title: Selected SALM (synaptic adhesion-like molecule) family proteins regulate synapse formation.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Drug-gene interactions and the search for missing heritability: a cross-sectional pharmacogenomics study of the QT interval.
    EBI GWAS Catalog
    Genome wide association study for plasma levels of natural anticoagulant inhibitors and protein C anticoagulant pathway: the MARTHA project.
    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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ30803, DKFZp686G0210

    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 negative regulation of inflammatory response IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of macrophage activation ISS
    Inferred from Sequence or Structural Similarity
    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
    is_active_in GABA-ergic synapse IBA
    Inferred from Biological aspect of Ancestor
    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
    		  
    is_active_in postsynaptic density membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    leucine-rich repeat and fibronectin type-III domain-containing protein 5
    Names
    fibronectin type III, immunoglobulin and leucine rich repeat domains 8

    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_051660.1 RefSeqGene

      Range
      5021..302694
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001330106.2 → NP_001317035.1  leucine-rich repeat and fibronectin type-III domain-containing protein 5 isoform 2 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate exon in the 3' coding region resulting in a frameshift compared to variant 1. The encoded isoform (2) has a shorter and distinct C-terminus compared to isoform 1. Variants 2 and 4 encode the same isoform.
      Source sequence(s)
      AL109662, AL121821, AL138498, AW013887
      Consensus CDS
      CCDS81800.1
      UniProtKB/TrEMBL
      G3V364, G3V4N1
      Related
      ENSP00000451067.1, ENST00000554171.1
      Conserved Domains (6) summary
      cd05764
      Location:301 → 374
      Ig_2; Subgroup of the immunoglobulin (Ig) superfamily
      cd00116
      Location:41 → 207
      LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...
      pfam07679
      Location:287 → 374
      I-set; Immunoglobulin I-set domain
      sd00033
      Location:53 → 76
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:99 → 159
      LRR_8; Leucine rich repeat
      cl15307
      Location:240 → 272
      TPKR_C2; Tyrosine-protein kinase receptor C2 Ig-like domain

    2. NM_001346173.2 → NP_001333102.1  leucine-rich repeat and fibronectin type-III domain-containing protein 5 isoform 1 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR comapred to variant 1. Variants 1 and 3 encode the same isoform (1).
      Source sequence(s)
      AL121821, AL138498, AW013887
      Consensus CDS
      CCDS9678.1
      UniProtKB/Swiss-Prot
      B3KU78, Q86XL2, Q96NI6
      UniProtKB/TrEMBL
      B4DS98

    3. NM_001346175.2 → NP_001333104.1  leucine-rich repeat and fibronectin type-III domain-containing protein 5 isoform 2 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR, and lacks an alternate exon in the 3' coding region resulting in a frameshift, compared to variant 1. The encoded isoform (2) has a shorter and distinct C-terminus compared to isoform 1. Variants 2 and 4 encode the same isoform.
      Source sequence(s)
      AL121821, AL138498, AW013887
      Consensus CDS
      CCDS81800.1
      UniProtKB/TrEMBL
      G3V364, G3V4N1

    4. NM_152447.5 → NP_689660.2  leucine-rich repeat and fibronectin type-III domain-containing protein 5 isoform 1 precursor

      See identical proteins and their annotated locations for NP_689660.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1). Variants 1 and 3 encode the same isoform.
      Source sequence(s)
      AK096627, AL121821, AL138498, AW013887, BC043165, DA096504
      Consensus CDS
      CCDS9678.1
      UniProtKB/Swiss-Prot
      B3KU78, Q86XL2, Q96NI6
      UniProtKB/TrEMBL
      B4DS98
      Related
      ENSP00000298119.4, ENST00000298119.9
      Conserved Domains (7) summary
      cd05764
      Location:301 → 374
      Ig_2; Subgroup of the immunoglobulin (Ig) superfamily
      smart00082
      Location:240 → 272
      LRRCT; Leucine rich repeat C-terminal domain
      cd00116
      Location:41 → 207
      LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...
      pfam07679
      Location:287 → 374
      I-set; Immunoglobulin I-set domain
      sd00033
      Location:53 → 76
      LRR_RI; leucine-rich repeat [structural motif]
      pfam00041
      Location:421 → 494
      fn3; Fibronectin type III domain
      pfam13855
      Location:99 → 159
      LRR_8; Leucine rich repeat

    RNA

    1. NR_144388.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) uses a different splice site in an internal exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AL109662, AL121821, AL138498, AW013887

    2. NR_144389.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) contains an alternate internal exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AL109662, AL121821, AL138498, AW013887

    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_000014.9 Reference GRCh38.p14 Primary Assembly

      Range
      41606876..41904549
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047431029.1 → XP_047286985.1  leucine-rich repeat and fibronectin type-III domain-containing protein 5 isoform X1

      UniProtKB/Swiss-Prot
      B3KU78, Q86XL2, Q96NI6
      UniProtKB/TrEMBL
      B4DS98

    RNA

    1. XR_007063991.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060938.1 Alternate T2T-CHM13v2.0

      Range
      35797646..36095321
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054375487.1 → XP_054231462.1  leucine-rich repeat and fibronectin type-III domain-containing protein 5 isoform X1

      UniProtKB/Swiss-Prot
      B3KU78, Q86XL2, Q96NI6
      UniProtKB/TrEMBL
      B4DS98
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96NI6.2 GenPept UniProtKB/Swiss-Prot:Q96NI6

    Gene LinkOut

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

    Chemical Information
    Molecular Biology Databases
    Research Materials
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