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    LRFN2 leucine rich repeat and fibronectin type III domain containing 2 [ Homo sapiens (human) ]

    Gene ID: 57497, updated on 4-Jan-2025

    Summary

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    Official Symbol
    LRFN2provided by HGNC
    Official Full Name
    leucine rich repeat and fibronectin type III domain containing 2provided by HGNC
    Primary source
    HGNC:HGNC:21226
    See related
    Ensembl:ENSG00000156564 MIM:612808; AllianceGenome:HGNC:21226
    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
    SALM1; FIGLER2; KIAA1246
    Summary
    Predicted to be involved in modulation of chemical synaptic transmission and regulation of postsynapse organization. Predicted to be located in plasma membrane. Predicted to be active in several cellular components, including Schaffer collateral - CA1 synapse; cell surface; and postsynaptic density membrane. [provided by Alliance of Genome Resources, Jan 2025]
    Expression
    Low expression observed in reference dataset See more
    Orthologs
    mouse all
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    Genomic context

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    See LRFN2 in Genome Data Viewer
    Location:
    6p21.2-p21.1
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (40391591..40587364, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (40219487..40415195, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (40359330..40555103, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:40311845-40312560 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:40313277-40313990 Neighboring gene long intergenic non-protein coding RNA 951 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr6:40327493-40328118 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:40346056-40347255 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:40377247-40377748 Neighboring gene testis development related 1 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:40386520-40387156 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:40387157-40387792 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:40387793-40388428 Neighboring gene RNA, U6 small nuclear 250, pseudogene Neighboring gene uncharacterized LOC105379699 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:40477543-40478043 Neighboring gene uncharacterized LOC105375051 Neighboring gene Sharpr-MPRA regulatory region 9042 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17169 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17170 Neighboring gene uncharacterized LOC101929535 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:40680899-40681400 Neighboring gene uncharacterized LOC105375052

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Dileucine and PDZ-binding motifs mediate synaptic adhesion-like molecule 1 (SALM1) trafficking in hippocampal neurons. Seabold GK, et al. J Biol Chem, 2012 Feb 10. PMID 22174418, Free PMC Article
    2. LRFN2 gene variant rs2494938 provides susceptibility to esophageal cancer in the population of Jammu and Kashmir. Shah R, et al. J Cancer Res Ther, 2020 Dec. PMID 32880595
    3. Bladder cancer intrinsic LRFN2 drives anticancer immunotherapy resistance by attenuating CD8(+) T cell infiltration and functional transition. Yu A, et al. J Immunother Cancer, 2023 Oct. PMID 37802603, Free PMC Article
    4. Heterozygous deletion of the LRFN2 gene is associated with working memory deficits. Thevenon J, et al. Eur J Hum Genet, 2016 Jun. PMID 26486473, Free PMC Article
    5. LRFN2 binding to NMDAR inhibits the progress of ESCC via regulating the Wnt/β-Catenin and NF-κB signaling pathway. Zhou Y, et al. Cancer Sci, 2022 Oct. PMID 35879265, Free PMC Article

    See all (22) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Bladder cancer intrinsic LRFN2 drives anticancer immunotherapy resistance by attenuating CD8[+] T cell infiltration and functional transition.
      Title: Bladder cancer intrinsic LRFN2 drives anticancer immunotherapy resistance by attenuating CD8(+) T cell infiltration and functional transition.
    2. LRFN2 binding to NMDAR inhibits the progress of ESCC via regulating the Wnt/beta-Catenin and NF-kappaB signaling pathway.
      Title: LRFN2 binding to NMDAR inhibits the progress of ESCC via regulating the Wnt/β-Catenin and NF-κB signaling pathway.
    3. LRFN2 gene variant rs2494938 provides susceptibility to esophageal cancer in the population of Jammu and Kashmir.
      Title: LRFN2 gene variant rs2494938 provides susceptibility to esophageal cancer in the population of Jammu and Kashmir.
    4. No significant association of variant rs2494938 of LRFN2 was observed with ovarian canceror breast cancer in a cohort of women in India.
      Title: Genetic variants of DNAH11 and LRFN2 genes and their association with ovarian and breast cancer.
    5. study demonstrated that the polymorphisms rs2494938 at 6p21.1 and rs2285947 at 7p15.3 may serve as independent prognostic biomarkers for ESCC, implying the potential biological role of their related genes (LRFN2 and DNAH11) in the process of ESCC development
      Title: Intronic polymorphisms in genes LRFN2 (rs2494938) and DNAH11 (rs2285947) are prognostic indicators of esophageal squamous cell carcinoma.
    6. Microdeletion encompassing LRFN2 gene segregates with working memory deficits and learning disabilities in three family members.
      Title: Heterozygous deletion of the LRFN2 gene is associated with working memory deficits.
    7. enrichment of SALM1 on the cell surface affects dendritic arborization, and intracellular motifs regulate its dendritic versus axonal localization.
      Title: Dileucine and PDZ-binding motifs mediate synaptic adhesion-like molecule 1 (SALM1) trafficking in hippocampal neurons.
    8. 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

    EBI GWAS Catalog

    Description
    A genome-wide association meta-analysis identifies a novel locus at 17q11.2 associated with sporadic amyotrophic lateral sclerosis.
    EBI GWAS Catalog
    Genetic variants at 6p21.1 and 7p15.3 are associated with risk of multiple cancers in Han Chinese.
    EBI GWAS Catalog
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    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)

    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

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in modulation of chemical synaptic transmission IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of postsynapse organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in Schaffer collateral - CA1 synapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in cell surface 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 presynapse 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 2
    Names
    fibronectin type III, immunoglobulin and leucine rich repeat domains 2
    synaptic adhesion-like molecule 1

    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_020737.3 → NP_065788.1  leucine-rich repeat and fibronectin type-III domain-containing protein 2 precursor

      Status: VALIDATED

      Source sequence(s)
      AB033072, AK291474, AL591063
      Consensus CDS
      CCDS34443.1
      UniProtKB/Swiss-Prot
      A5PKU3, Q5SYP9, Q9ULH4
      UniProtKB/TrEMBL
      A0A8V8TQ63
      Related
      ENSP00000345985.6, ENST00000338305.7
      Conserved Domains (5) summary
      smart00082
      Location:242 → 286
      LRRCT; Leucine rich repeat C-terminal domain
      sd00033
      Location:54 → 77
      LRR_RI; leucine-rich repeat [structural motif]
      pfam00041
      Location:420 → 493
      fn3; Fibronectin type III domain
      pfam13855
      Location:76 → 136
      LRR_8; Leucine rich repeat
      cl11960
      Location:303 → 376
      Ig; Immunoglobulin domain

    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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      40391591..40587364 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011514762.3 → XP_011513064.1  leucine-rich repeat and fibronectin type-III domain-containing protein 2 isoform X1

      UniProtKB/Swiss-Prot
      A5PKU3, Q5SYP9, Q9ULH4
      UniProtKB/TrEMBL
      A0A8V8TQ63
      Conserved Domains (5) summary
      smart00082
      Location:242 → 286
      LRRCT; Leucine rich repeat C-terminal domain
      sd00033
      Location:54 → 77
      LRR_RI; leucine-rich repeat [structural motif]
      pfam00041
      Location:420 → 493
      fn3; Fibronectin type III domain
      pfam13855
      Location:76 → 136
      LRR_8; Leucine rich repeat
      cl11960
      Location:303 → 376
      Ig; Immunoglobulin domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      40219487..40415195 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054356062.1 → XP_054212037.1  leucine-rich repeat and fibronectin type-III domain-containing protein 2 isoform X1

      UniProtKB/Swiss-Prot
      A5PKU3, Q5SYP9, Q9ULH4
      UniProtKB/TrEMBL
      A0A8V8TQ63
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9ULH4.2 GenPept UniProtKB/Swiss-Prot:Q9ULH4

    Gene LinkOut

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