U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination
    • Showing Current items.

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

    Gene ID: 57497, updated on 17-Jun-2024

    Summary

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    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

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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

    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)

    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_020737.3NP_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:242286
      LRRCT; Leucine rich repeat C-terminal domain
      sd00033
      Location:5477
      LRR_RI; leucine-rich repeat [structural motif]
      pfam00041
      Location:420493
      fn3; Fibronectin type III domain
      pfam13855
      Location:76136
      LRR_8; Leucine rich repeat
      cl11960
      Location:303376
      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_011514762.3XP_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:242286
      LRRCT; Leucine rich repeat C-terminal domain
      sd00033
      Location:5477
      LRR_RI; leucine-rich repeat [structural motif]
      pfam00041
      Location:420493
      fn3; Fibronectin type III domain
      pfam13855
      Location:76136
      LRR_8; Leucine rich repeat
      cl11960
      Location:303376
      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_054356062.1XP_054212037.1  leucine-rich repeat and fibronectin type-III domain-containing protein 2 isoform X1

      UniProtKB/Swiss-Prot
      A5PKU3, Q5SYP9, Q9ULH4
      UniProtKB/TrEMBL
      A0A8V8TQ63