Aliases for LRFN2 Gene

Aliases for LRFN2 Gene

  • Leucine Rich Repeat And Fibronectin Type III Domain Containing 2 2 3 5
  • KIAA1246 2 3 4
  • Leucine-Rich Repeat And Fibronectin Type-III Domain-Containing Protein 2 3 4
  • Fibronectin Type III, Immunoglobulin And Leucine Rich Repeat Domains 2 2 3
  • Synaptic Adhesion-Like Molecule 1 3 4
  • SALM1 3 4
  • FIGLER2 3

External Ids for LRFN2 Gene

Previous HGNC Symbols for LRFN2 Gene

  • KIAA1246
  • SALM1

Previous GeneCards Identifiers for LRFN2 Gene

  • GC06M040406
  • GC06M040467
  • GC06M040077
  • GC06M040661
  • GC06M040518

Summaries for LRFN2 Gene

GeneCards Summary for LRFN2 Gene

LRFN2 (Leucine Rich Repeat And Fibronectin Type III Domain Containing 2) is a Protein Coding gene. Diseases associated with LRFN2 include Neuronitis. Among its related pathways are Protein-protein interactions at synapses and Transmission across Chemical Synapses. An important paralog of this gene is LRFN5.

UniProtKB/Swiss-Prot Summary for LRFN2 Gene

  • Promotes neurite outgrowth in hippocampal neurons. Enhances the cell surface expression of 2 NMDA receptor subunits GRIN1 and GRIN2A. May play a role in redistributing DLG4 to the cell periphery (By similarity).

Additional gene information for LRFN2 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for LRFN2 Gene

Genomics for LRFN2 Gene

GeneHancer (GH) Regulatory Elements for LRFN2 Gene

Promoters and enhancers for LRFN2 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH06J040587 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE CraniofacialAtlas 505.7 +0.1 63 1.6 EP300 CTCF USF1 RBAK ZNF639 ZIC2 ZBTB10 ZNF423 ZBTB26 KLF7 LRFN2 NFYA piR-39858-553
GH06J040585 Enhancer 0.6 ENCODE 500.7 +1.7 1727 0.1 TEAD4 ZIC2 ZNF341 POLR2A YY1 SIN3A GLIS1 ZNF398 SMARCA4 MAZ LRFN2 piR-39858-553
GH06J040581 Promoter 0.3 EPDnew 500.4 +5.6 5582 0.1 LRFN2 piR-39858-553
GH06J040524 Enhancer 0.6 Ensembl 31 +62.6 62563 3 EP300 HDAC2 RBM25 JUND ZNF768 RXRA HNF4A ZMYM3 BCL3 ZFP36 ENSG00000226454 LOC105375051 LRFN2 piR-39858-553
GH06J040543 Enhancer 0.6 Ensembl ENCODE 28.8 +44.4 44363 3.8 FOS GATA2 EGR2 POLR2A SOX6 LRFN2 ENSG00000226454 DAAM2 LOC105375051 piR-39858-553
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LRFN2 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for LRFN2

Top Transcription factor binding sites by QIAGEN in the LRFN2 gene promoter:
  • AP-1
  • C/EBPalpha
  • CREB
  • Evi-1
  • FOXO3
  • FOXO3a
  • FOXO3b
  • HOXA9
  • HOXA9B
  • MZF-1

Genomic Locations for LRFN2 Gene

Genomic Locations for LRFN2 Gene
chr6:40,391,099-40,587,464
(GRCh38/hg38)
Size:
196,366 bases
Orientation:
Minus strand
chr6:40,359,325-40,555,204
(GRCh37/hg19)
Size:
195,880 bases
Orientation:
Minus strand

Genomic View for LRFN2 Gene

Genes around LRFN2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LRFN2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LRFN2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LRFN2 Gene

Proteins for LRFN2 Gene

  • Protein details for LRFN2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9ULH4-LRFN2_HUMAN
    Recommended name:
    Leucine-rich repeat and fibronectin type-III domain-containing protein 2
    Protein Accession:
    Q9ULH4
    Secondary Accessions:
    • A5PKU3
    • Q5SYP9

    Protein attributes for LRFN2 Gene

    Size:
    789 amino acids
    Molecular mass:
    84731 Da
    Quaternary structure:
    • Forms heteromeric complexes with LRFN1, LRFN3, LRFN4 and LRFN5. Can form homomeric complexes, but not across cell junctions. Directly interacts with 2 NMDA receptor subunits GRIN1 and GRIN2A (By similarity). Interacts with DLG1, DLG2, DLG3 and DLG4.
    SequenceCaution:
    • Sequence=BAA86560.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};

neXtProt entry for LRFN2 Gene

Post-translational modifications for LRFN2 Gene

Other Protein References for LRFN2 Gene

No data available for DME Specific Peptides for LRFN2 Gene

Domains & Families for LRFN2 Gene

Protein Domains for LRFN2 Gene

Blocks:
  • Immunoglobulin C-2 type
  • Immunoglobulin I-set
  • Cysteine-rich flanking region, C-terminal
  • Cysteine-rich flanking region, N-terminal
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for LRFN2 Gene

GenScript: Design optimal peptide antigens:
  • Synaptic adhesion-like molecule 1 (LRFN2_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9ULH4

UniProtKB/Swiss-Prot:

LRFN2_HUMAN :
  • The PDZ-binding motif is required for cell surface expression, neurite outgrowth promotion (By similarity). This motif is also involved in DLG1-, DLG3- and DLG4-binding.
  • Belongs to the LRFN family.
Domain:
  • The PDZ-binding motif is required for cell surface expression, neurite outgrowth promotion (By similarity). This motif is also involved in DLG1-, DLG3- and DLG4-binding.
Family:
  • Belongs to the LRFN family.
genes like me logo Genes that share domains with LRFN2: view

Function for LRFN2 Gene

Molecular function for LRFN2 Gene

UniProtKB/Swiss-Prot Function:
Promotes neurite outgrowth in hippocampal neurons. Enhances the cell surface expression of 2 NMDA receptor subunits GRIN1 and GRIN2A. May play a role in redistributing DLG4 to the cell periphery (By similarity).

Phenotypes From GWAS Catalog for LRFN2 Gene

genes like me logo Genes that share phenotypes with LRFN2: view

Animal Models for LRFN2 Gene

MGI Knock Outs for LRFN2:

Animal Model Products

  • Taconic Biosciences Mouse Models for LRFN2

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LRFN2

Clone Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , miRNA , Transcription Factor Targets and HOMER Transcription for LRFN2 Gene

Localization for LRFN2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LRFN2 Gene

Membrane; Single-pass type I membrane protein. Cell junction, synapse. Cell junction, synapse, postsynaptic cell membrane.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for LRFN2 gene
Compartment Confidence
plasma membrane 5
extracellular 2
cytoskeleton 1
nucleus 1
endoplasmic reticulum 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for LRFN2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0009986 cell surface IEA,IBA 21873635
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0030054 cell junction IEA --
genes like me logo Genes that share ontologies with LRFN2: view

Pathways & Interactions for LRFN2 Gene

genes like me logo Genes that share pathways with LRFN2: view

Pathways by source for LRFN2 Gene

Gene Ontology (GO) - Biological Process for LRFN2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0050804 modulation of chemical synaptic transmission IEA --
GO:0099175 regulation of postsynapse organization IEA --
genes like me logo Genes that share ontologies with LRFN2: view

No data available for SIGNOR curated interactions for LRFN2 Gene

Drugs & Compounds for LRFN2 Gene

No Compound Related Data Available

Transcripts for LRFN2 Gene

mRNA/cDNA for LRFN2 Gene

1 REFSEQ mRNAs :
4 NCBI additional mRNA sequence :
1 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LRFN2

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for LRFN2 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7
SP1: - - - -
SP2:
SP3:

Relevant External Links for LRFN2 Gene

GeneLoc Exon Structure for
LRFN2

Expression for LRFN2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for LRFN2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for LRFN2 Gene

This gene is overexpressed in Brain - Cortex (x10.1), Brain - Frontal Cortex (BA9) (x8.4), Brain - Anterior cingulate cortex (BA24) (x7.1), Brain - Amygdala (x4.1), and Brain - Hippocampus (x4.0).

Protein differential expression in normal tissues from HIPED for LRFN2 Gene

This gene is overexpressed in Spinal cord (26.5), Adipocyte (15.2), Fetal Brain (9.4), and Pancreatic juice (8.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for LRFN2 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LRFN2

SOURCE GeneReport for Unigene cluster for LRFN2 Gene:

Hs.250015

Evidence on tissue expression from TISSUES for LRFN2 Gene

  • Nervous system(4.6)
genes like me logo Genes that share expression patterns with LRFN2: view

No data available for Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for LRFN2 Gene

Orthologs for LRFN2 Gene

This gene was present in the common ancestor of chordates.

Orthologs for LRFN2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LRFN2 31 30
  • 98.53 (n)
OneToOne
dog
(Canis familiaris)
Mammalia LRFN2 31 30
  • 91 (n)
OneToOne
cow
(Bos Taurus)
Mammalia LRFN2 31 30
  • 90.51 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia LRFN2 31
  • 87 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Lrfn2 17 31 30
  • 86.95 (n)
rat
(Rattus norvegicus)
Mammalia Lrfn2 30
  • 86.66 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia LRFN2 31
  • 82 (a)
OneToOne
chicken
(Gallus gallus)
Aves LRFN2 31 30
  • 72.85 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia LRFN2 31
  • 80 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100491687 30
  • 69.98 (n)
zebrafish
(Danio rerio)
Actinopterygii LRFN2 (1 of 2) 31
  • 68 (a)
OneToMany
LRFN2 (2 of 2) 31
  • 65 (a)
OneToMany
LOC797812 30
  • 64.71 (n)
Species where no ortholog for LRFN2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for LRFN2 Gene

ENSEMBL:
Gene Tree for LRFN2 (if available)
TreeFam:
Gene Tree for LRFN2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LRFN2: view image

Paralogs for LRFN2 Gene

(4) SIMAP similar genes for LRFN2 Gene using alignment to 1 proteins:

  • LRFN2_HUMAN
genes like me logo Genes that share paralogs with LRFN2: view

Variants for LRFN2 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for LRFN2 Gene

SNP ID Clinical significance and condition Chr 06 pos Variation AA Info Type
728592 Benign: not provided 40,392,096(-) C/A SYNONYMOUS_VARIANT
rs3734559 - p.Asp770Asn

Additional dbSNP identifiers (rs#s) for LRFN2 Gene

Structural Variations from Database of Genomic Variants (DGV) for LRFN2 Gene

Variant ID Type Subtype PubMed ID
esv2657085 CNV deletion 23128226
esv2674055 CNV deletion 23128226
esv2678163 CNV deletion 23128226
esv2731968 CNV deletion 23290073
esv2731969 CNV deletion 23290073
esv2731970 CNV deletion 23290073
esv2763989 CNV loss 21179565
esv28480 CNV loss 19812545
esv3567686 CNV deletion 23714750
esv3567687 CNV deletion 23714750
esv3567690 CNV deletion 23714750
esv3571024 CNV loss 25503493
esv3571025 CNV loss 25503493
esv3608772 CNV loss 21293372
esv3608774 CNV loss 21293372
esv3608775 CNV loss 21293372
esv3608776 CNV loss 21293372
nsv348769 CNV deletion 16902084
nsv476961 CNV novel sequence insertion 20440878
nsv519241 CNV gain 19592680
nsv525098 CNV loss 19592680
nsv5273 CNV deletion 18451855
nsv602966 CNV loss 21841781

Variation tolerance for LRFN2 Gene

Residual Variation Intolerance Score: 10.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.52; 71.96% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LRFN2 Gene

Human Gene Mutation Database (HGMD)
LRFN2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
LRFN2

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LRFN2 Gene

Disorders for LRFN2 Gene

MalaCards: The human disease database

(1) MalaCards diseases for LRFN2 Gene - From: DISEASES

Disorder Aliases PubMed IDs
neuronitis
- elite association - COSMIC cancer census association via MalaCards
Search LRFN2 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for LRFN2

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with LRFN2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for LRFN2 Gene

Publications for LRFN2 Gene

  1. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 41 54
  2. Comparative analysis of structure, expression and PSD95-binding capacity of Lrfn, a novel family of neuronal transmembrane proteins. (PMID: 16828986) Morimura N … Aruga J (Gene 2006) 2 3 54
  3. A novel family of adhesion-like molecules that interacts with the NMDA receptor. (PMID: 16495444) Wang CY … Wenthold RJ (The Journal of neuroscience : the official journal of the Society for Neuroscience 2006) 2 3 54
  4. The DNA sequence and analysis of human chromosome 6. (PMID: 14574404) Mungall AJ … Beck S (Nature 2003) 3 4 54
  5. Prediction of the coding sequences of unidentified human genes. XV. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 10574462) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 1999) 3 4 54

Products for LRFN2 Gene

Sources for LRFN2 Gene