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

Gene ID: 145581, updated on 11-Apr-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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Location:
14q21.1
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (41606876..41904549)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (35797646..36095321)
105.20220307 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. LRFN5 and OLFM4 as novel potential biomarkers for major depressive disorder: a pilot study. Xu K, et al. Transl Psychiatry, 2023 Jun 6. PMID 37280213, Free PMC Article
  5. Structural basis of SALM5-induced PTPδ dimerization for synaptic differentiation. Lin Z, et al. Nat Commun, 2018 Jan 18. PMID 29348579, 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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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
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)

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

  • 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
  
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 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_2023_10

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

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
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96NI6.2 GenPept UniProtKB/Swiss-Prot:Q96NI6

Gene LinkOut

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