U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

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

    Gene ID: 57497, updated on 11-Apr-2024

    Summary

    Go to the top of the page Help
    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 Schaffer collateral - CA1 synapse and cell surface. Predicted to be integral component of postsynaptic density membrane. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Low expression observed in reference dataset See more
    Orthologs
    mouse all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See LRFN2 in Genome Data Viewer
    Location:
    6p21.2-p21.1
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (40391591..40587364, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (40219487..40415195, complement)
    105.20220307 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

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    Related articles in PubMed

    1. 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
    2. 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
    3. 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
    4. 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
    5. Genetic variants of DNAH11 and LRFN2 genes and their association with ovarian and breast cancer. Verma S, et al. Int J Gynaecol Obstet, 2020 Jan. PMID 31605628

    See all (21) 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

    Go to the top of the page Help

    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

    Go to the top of the page Help

    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

    Go to the top of the page

    Interactions

    Go to the top of the page Help
    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Go to the top of the page Help

    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 postsynaptic membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in presynapse IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

    Go to the top of the page Help
    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)

    Go to the top of the page Help

    NEW Try the new Transcript table

    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

      See identical proteins and their annotated locations for NP_065788.1

      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_2023_10

    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

      See identical proteins and their annotated locations for XP_011513064.1

      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
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9ULH4.2 GenPept UniProtKB/Swiss-Prot:Q9ULH4

    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
    Tools
    Miscellaneous