This gene encodes a protein that has a fibronectin type III domain and a C-terminal transmembrane domain, as well as a leucine-rich repeat domain and immunoglobulin-like domain near the N-terminus. The encoded protein may regulate fibroblast growth factor receptors and affect the modification of these receptors, which are glycosylated differently in the Golgi and endoplasmic re... See more...

Aliases for LRIT3 Gene

Aliases for LRIT3 Gene

  • Leucine Rich Repeat, Ig-Like And Transmembrane Domains 3 2 3 5
  • Leucine-Rich Repeat, Immunoglobulin-Like Domain And Transmembrane Domain-Containing Protein 3 3 4
  • Fibronectin Type III, Immunoglobulin And Leucine Rich Repeat Domains 4 2 3
  • FIGLER4 2 3
  • CSNB1F 2 3
  • Leucine-Rich Repeat, Immunoglobulin-Like And Transmembrane Domains 3 3
  • FLJ44691 2
  • LRIT3 5

External Ids for LRIT3 Gene

Previous GeneCards Identifiers for LRIT3 Gene

  • GC04P110992
  • GC04P110772
  • GC04P106504

Summaries for LRIT3 Gene

Entrez Gene Summary for LRIT3 Gene

  • This gene encodes a protein that has a fibronectin type III domain and a C-terminal transmembrane domain, as well as a leucine-rich repeat domain and immunoglobulin-like domain near the N-terminus. The encoded protein may regulate fibroblast growth factor receptors and affect the modification of these receptors, which are glycosylated differently in the Golgi and endoplasmic reticulum. Mutations in this gene are associated with congenital stationary night blindness, type 1F. [provided by RefSeq, May 2013]

GeneCards Summary for LRIT3 Gene

LRIT3 (Leucine Rich Repeat, Ig-Like And Transmembrane Domains 3) is a Protein Coding gene. Diseases associated with LRIT3 include Night Blindness, Congenital Stationary, Type 1F and Congenital Stationary Night Blindness. An important paralog of this gene is LRIT1.

UniProtKB/Swiss-Prot Summary for LRIT3 Gene

  • Plays a role in the synapse formation and synaptic transmission between cone photoreceptor cells and retinal bipolar cells (By similarity). Required for normal transmission of a light-evoked stimulus from the cone photoreceptor cells to the ON-bipolar cells and ON-ganglion cells in the inner retina (PubMed:28334377). Required in retinal ON-bipolar cells for normal localization of the cation channel TRPM1 at dendrite tips (By similarity). Seems to play a specific role in synaptic contacts made by ON-bipolar cells with cone photoreceptor pedicles (By similarity). May also have a role in cone synapse formation (By similarity). Might facilitate FGFR1 exit from the endoplasmic reticulum to the Golgi (PubMed:22673519). Could be a regulator of the FGFRs (PubMed:22673519).

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for LRIT3 Gene

Genomics for LRIT3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for LRIT3 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
GH04J109846 Enhancer 0.3 Ensembl 600.7 -1.5 -1506 0.8 IKZF1 LRIT3 GAR1 EGF piR-38051-203 RRH
GH04J109848 Enhancer 0.3 Ensembl 600.7 +0.4 394 0.6 RNF2 LRIT3 EGF RRH HSALNG0036345
GH04J109814 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 7.7 -32.0 -31983 3.1 CREB1 GATAD2A PRDM10 REST ZNF629 RFX1 LEF1 POLR2A TARDBP ZHX2 GAR1 ENSG00000272795 SETP20 SEC24B CDC42P4 CASP6 LRIT3 lnc-CFI-2 RRH
GH04J109912 Promoter/Enhancer 1.4 EPDnew Ensembl ENCODE 10.4 +66.4 66432 4.6 IKZF1 JUND PRDM1 PKNOX1 REST BRD9 GTF2E2 CTBP1 NFE2 HDAC2 EGF LRIT3 HSALNG0036348 ELOVL6
GH04J109980 Promoter/Enhancer 1.1 EPDnew Ensembl ENCODE 10.2 +131.5 131480 3.2 CTCF ARID3A PRDM10 RAD21 SMC3 TEAD1 ZNF335 MAFK ZNF654 CEBPB EGF HSALNG0036348 ENSG00000250511 LRIT3 GAR1 ELOVL6
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LRIT3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for LRIT3

Top Transcription factor binding sites by QIAGEN in the LRIT3 gene promoter:
  • GCNF
  • GCNF-1
  • GCNF-2
  • GR
  • GR-alpha
  • GR-beta
  • RORalpha2
  • RP58
  • SRF
  • SRF (504 AA)

Genomic Locations for LRIT3 Gene

Genomic Locations for LRIT3 Gene
chr4:109,848,107-109,872,315
(GRCh38/hg38)
Size:
24,209 bases
Orientation:
Plus strand
chr4:110,769,358-110,793,471
(GRCh37/hg19)
Size:
24,114 bases
Orientation:
Plus strand

Genomic View for LRIT3 Gene

Genes around LRIT3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LRIT3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LRIT3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LRIT3 Gene

Proteins for LRIT3 Gene

  • Protein details for LRIT3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q3SXY7-LRIT3_HUMAN
    Recommended name:
    Leucine-rich repeat, immunoglobulin-like domain and transmembrane domain-containing protein 3
    Protein Accession:
    Q3SXY7
    Secondary Accessions:
    • C9J1C2
    • Q6ZTG1

    Protein attributes for LRIT3 Gene

    Size:
    679 amino acids
    Molecular mass:
    74754 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAI04038.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};

    Alternative splice isoforms for LRIT3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for LRIT3 Gene

Post-translational modifications for LRIT3 Gene

Other Protein References for LRIT3 Gene

No data available for DME Specific Peptides for LRIT3 Gene

Domains & Families for LRIT3 Gene

Gene Families for LRIT3 Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted membrane proteins

Protein Domains for LRIT3 Gene

Suggested Antigen Peptide Sequences for LRIT3 Gene

GenScript: Design optimal peptide antigens:
  • Leucine-rich repeat, immunoglobulin-like domain and transmembrane domain-containing protein 3 (LRIT3_HUMAN)
genes like me logo Genes that share domains with LRIT3: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for LRIT3 Gene

Function for LRIT3 Gene

Molecular function for LRIT3 Gene

UniProtKB/Swiss-Prot Function:
Plays a role in the synapse formation and synaptic transmission between cone photoreceptor cells and retinal bipolar cells (By similarity). Required for normal transmission of a light-evoked stimulus from the cone photoreceptor cells to the ON-bipolar cells and ON-ganglion cells in the inner retina (PubMed:28334377). Required in retinal ON-bipolar cells for normal localization of the cation channel TRPM1 at dendrite tips (By similarity). Seems to play a specific role in synaptic contacts made by ON-bipolar cells with cone photoreceptor pedicles (By similarity). May also have a role in cone synapse formation (By similarity). Might facilitate FGFR1 exit from the endoplasmic reticulum to the Golgi (PubMed:22673519). Could be a regulator of the FGFRs (PubMed:22673519).

Phenotypes From GWAS Catalog for LRIT3 Gene

Gene Ontology (GO) - Molecular Function for LRIT3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IEA --
genes like me logo Genes that share ontologies with LRIT3: view

Phenotypes for LRIT3 Gene

genes like me logo Genes that share phenotypes with LRIT3: view

Human Phenotype Ontology for LRIT3 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

  • Taconic Biosciences Mouse Models for LRIT3

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LRIT3

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for LRIT3 Gene

Localization for LRIT3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LRIT3 Gene

Cell projection, dendrite. Perikaryon. Endoplasmic reticulum membrane. Single-pass type I membrane protein. Note=Punctate expression at dendrite tips. {ECO:0000269 PubMed:23246293}.

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 LRIT3 gene
Compartment Confidence
endoplasmic reticulum 3
plasma membrane 2
mitochondrion 2
nucleus 2
cytosol 2
extracellular 1
cytoskeleton 1
peroxisome 0
golgi apparatus 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Mitochondria (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for LRIT3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005783 endoplasmic reticulum IEA --
GO:0005789 endoplasmic reticulum membrane IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0030425 dendrite IEA --
genes like me logo Genes that share ontologies with LRIT3: view

Pathways & Interactions for LRIT3 Gene

PathCards logo

SuperPathways for LRIT3 Gene

No Data Available

Interacting Proteins for LRIT3 Gene

Gene Ontology (GO) - Biological Process for LRIT3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007601 visual perception IEA --
GO:0040036 regulation of fibroblast growth factor receptor signaling pathway IDA 22673519
GO:0050896 response to stimulus IEA --
genes like me logo Genes that share ontologies with LRIT3: view

No data available for Pathways by source and SIGNOR curated interactions for LRIT3 Gene

Drugs & Compounds for LRIT3 Gene

No Compound Related Data Available

Transcripts for LRIT3 Gene

mRNA/cDNA for LRIT3 Gene

1 REFSEQ mRNAs :
6 NCBI additional mRNA sequence :
2 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 LRIT3

Alternative Splicing Database (ASD) splice patterns (SP) for LRIT3 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4a · 4b
SP1:
SP2: -

Relevant External Links for LRIT3 Gene

GeneLoc Exon Structure for
LRIT3

Expression for LRIT3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for LRIT3 Gene

Protein differential expression in normal tissues from HIPED for LRIT3 Gene

This gene is overexpressed in Serum (61.2) and Retina (7.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for LRIT3 Gene



Protein tissue co-expression partners for LRIT3 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LRIT3

SOURCE GeneReport for Unigene cluster for LRIT3 Gene:

Hs.308127

mRNA Expression by UniProt/SwissProt for LRIT3 Gene:

Q3SXY7-LRIT3_HUMAN
Tissue specificity: Detected in the outer plexiform layer (OPL) of the retina where it localizes to ON-bipolar cells (at protein level).

Evidence on tissue expression from TISSUES for LRIT3 Gene

  • Nervous system(4.4)
  • Eye(2.3)

Phenotype-based relationships between genes and organs from Gene ORGANizer for LRIT3 Gene

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • immune
  • integumentary
  • nervous
  • skeletal muscle
Regions:
Head and neck:
  • brain
  • cranial nerve
  • eye
  • head
General:
  • blood
  • peripheral nervous system
  • skin
  • white blood cell
genes like me logo Genes that share expression patterns with LRIT3: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for LRIT3 Gene

Orthologs for LRIT3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for LRIT3 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia LRIT3 30 31
  • 99.66 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia LRIT3 30 31
  • 85.03 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia LRIT3 30 31
  • 81.9 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Lrit3 30
  • 77.43 (n)
Mouse
(Mus musculus)
Mammalia Lrit3 30 17 31
  • 77.1 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia LRIT3 31
  • 61 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia LRIT3 31
  • 55 (a)
OneToOne
Chicken
(Gallus gallus)
Aves LRIT3 30 31
  • 65.88 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia LRIT3 31
  • 55 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia lrit3 30
  • 67.71 (n)
Zebrafish
(Danio rerio)
Actinopterygii lrit3a 30 31
  • 64.64 (n)
OneToOne
Species where no ortholog for LRIT3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (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 LRIT3 Gene

ENSEMBL:
Gene Tree for LRIT3 (if available)
TreeFam:
Gene Tree for LRIT3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LRIT3: view image

Paralogs for LRIT3 Gene

(4) SIMAP similar genes for LRIT3 Gene using alignment to 1 proteins:

  • LRIT3_HUMAN
genes like me logo Genes that share paralogs with LRIT3: view

Variants for LRIT3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for LRIT3 Gene

SNP ID Clinical significance and condition Chr 04 pos Variation AA Info Type
684455 Uncertain Significance: Congenital stationary night blindness, type 1F 109,867,784(+) C/T MISSENSE_VARIANT
727796 Likely Benign: not provided 109,870,675(+) C/T SYNONYMOUS_VARIANT
728146 Benign: not provided 109,851,791(+) A/T MISSENSE_VARIANT
735145 Likely Benign: not provided 109,851,912(+) C/T SYNONYMOUS_VARIANT
737160 Conflicting Interpretations: Congenital stationary night blindness, type 1F; not provided 109,851,609(+) G/A SYNONYMOUS_VARIANT

Additional dbSNP identifiers (rs#s) for LRIT3 Gene

Variation tolerance for LRIT3 Gene

Residual Variation Intolerance Score: 73.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 21.61; 99.31% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LRIT3 Gene

Human Gene Mutation Database (HGMD)
LRIT3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
LRIT3

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for LRIT3 Gene

Disorders for LRIT3 Gene

MalaCards: The human disease database

(9) MalaCards diseases for LRIT3 Gene - From: UniProtKB/Swiss-Prot, OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search LRIT3 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

LRIT3_HUMAN
  • Night blindness, congenital stationary, 1F (CSNB1F) [MIM:615058]: An autosomal recessive form of congenital stationary night blindness, a non-progressive retinal disorder characterized by impaired night vision, often associated with nystagmus and myopia. {ECO:0000269 PubMed:23246293, ECO:0000269 PubMed:27428514}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for LRIT3

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with LRIT3: view

No data available for Genatlas for LRIT3 Gene

Publications for LRIT3 Gene

  1. Mutation screening of the LRIT3, CABP4, and GPR179 genes in Chinese patients with Schubert-Bornschein congenital stationary night blindness. (PMID: 27428514) Dan H … Li T (Ophthalmic genetics 2017) 3 4
  2. LRIT3 Differentially Affects Connectivity and Synaptic Transmission of Cones to ON- and OFF-Bipolar Cells. (PMID: 28334377) Neuillé M … Zeitz C (Investigative ophthalmology & visual science 2017) 3 4
  3. Whole-exome sequencing identifies LRIT3 mutations as a cause of autosomal-recessive complete congenital stationary night blindness. (PMID: 23246293) Zeitz C … Audo I (American journal of human genetics 2013) 3 4
  4. Leucine-rich repeat, immunoglobulin-like and transmembrane domain 3 (LRIT3) is a modulator of FGFR1. (PMID: 22673519) Kim SD … Kim J (FEBS letters 2012) 3 4
  5. A systematic gene-based screen of chr4q22-q32 identifies association of a novel susceptibility gene, DKK2, with the quantitative trait of alcohol dependence symptom counts. (PMID: 20332099) Kalsi G … Riley BP (Human molecular genetics 2010) 3 41

Products for LRIT3 Gene

  • Signalway ELISA kits for LRIT3

Sources for LRIT3 Gene