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Aliases for LRIT3 Gene

Aliases for LRIT3 Gene

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

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 for LRIT3 Gene

  • Required in retinal ON-bipolar cells for normal localization of the cation channel TRPM1 at dendrite tips (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).

Additional gene information for LRIT3 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LRIT3 Gene

Genomics for LRIT3 Gene

GeneHancer (GH) Regulatory Elements for LRIT3 Gene

Promoters and enhancers for LRIT3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH04I109848 Promoter 0.6 EPDnew 550.8 -0.1 -96 0.1 BMI1 LRIT3 EGF RRH
GH04I109912 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE 10.4 +66.4 66355 4.6 PKNOX1 LEF1 NFATC3 GTF2E2 JUN FOSL1 CC2D1A CTBP1 ZNF316 POLR2A EGF LRIT3 GC04P109993
GH04I109814 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 7.7 -32.1 -32060 3.1 FOXA2 CLOCK SMAD1 ARNT ARID4B SIN3A FEZF1 DMAP1 YY1 POLR2B GAR1 ENSG00000272795 SETP20 SEC24B CDC42P4 CASP6 LRIT3 GC04M109825
GH04I109422 Enhancer 1 Ensembl ENCODE 9.3 -425.5 -425493 0.6 HDGF PKNOX1 ATF1 ZNF2 RAD21 ARID2 ZNF143 CREM MIXL1 DEK SEC24B CDC42P4 SETP20 CASP6 GAR1 OSTC PLA2G12A LRIT3 SEC24B-AS1 PIR37678
GH04I109801 Promoter/Enhancer 1.3 EPDnew ENCODE 5.2 -46.1 -46091 2.1 FEZF1 RAD21 RARA YY1 MIXL1 RXRA NFYC KAT8 NFIL3 NFIC CFI LRIT3 GAR1 PLA2G12A
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around LRIT3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the LRIT3 gene promoter:

Genomic Locations for LRIT3 Gene

Genomic Locations for LRIT3 Gene
24,132 bases
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:
    Recommended name:
    Leucine-rich repeat, immunoglobulin-like domain and transmembrane domain-containing protein 3
    Protein Accession:
    Secondary Accessions:
    • C9J1C2
    • Q6ZTG1

    Protein attributes for LRIT3 Gene

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

    Alternative splice isoforms for LRIT3 Gene


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

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

Suggested Antigen Peptide Sequences for LRIT3 Gene

Graphical View of Domain Structure for InterPro Entry

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

No data available for UniProtKB/Swiss-Prot for LRIT3 Gene

Function for LRIT3 Gene

Molecular function for LRIT3 Gene

UniProtKB/Swiss-Prot Function:
Required in retinal ON-bipolar cells for normal localization of the cation channel TRPM1 at dendrite tips (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

Phenotypes for LRIT3 Gene

MGI mutant phenotypes for LRIT3:
inferred from 2 alleles
GenomeRNAi human phenotypes for LRIT3:
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

Clone Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , 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

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 4
plasma membrane 2
mitochondrion 2
nucleus 2
cytosol 2
peroxisome 1
golgi apparatus 1

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:0005789 endoplasmic reticulum membrane IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0030425 dendrite IEA --
GO:0042995 cell projection IEA --
genes like me logo Genes that share ontologies with LRIT3: view

Pathways & Interactions for LRIT3 Gene

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

(3) REFSEQ mRNAs :
(3) Additional mRNA sequences :
(4) Selected AceView cDNA sequences:
(2) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for LRIT3 Gene

Leucine-rich repeat, immunoglobulin-like and transmembrane domains 3:
Representative Sequences:

Clone Products

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

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

Relevant External Links for LRIT3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for LRIT3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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

NURSA nuclear receptor signaling pathways regulating expression of LRIT3 Gene:


SOURCE GeneReport for Unigene cluster for LRIT3 Gene:


mRNA Expression by UniProt/SwissProt for LRIT3 Gene:

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(4.3)

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

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

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
(Pan troglodytes)
Mammalia LRIT3 33 34
  • 99.66 (n)
(Canis familiaris)
Mammalia LRIT3 33 34
  • 85.03 (n)
(Bos Taurus)
Mammalia LRIT3 33 34
  • 81.9 (n)
(Rattus norvegicus)
Mammalia Lrit3 33
  • 77.43 (n)
(Mus musculus)
Mammalia Lrit3 33 16 34
  • 77.1 (n)
(Monodelphis domestica)
Mammalia LRIT3 34
  • 61 (a)
(Ornithorhynchus anatinus)
Mammalia LRIT3 34
  • 55 (a)
(Gallus gallus)
Aves LRIT3 33 34
  • 65.88 (n)
(Anolis carolinensis)
Reptilia LRIT3 34
  • 55 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia lrit3 33
  • 67.71 (n)
(Danio rerio)
Actinopterygii lrit3a 33 34
  • 64.64 (n)
Species where no ortholog for LRIT3 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 LRIT3 Gene

Gene Tree for LRIT3 (if available)
Gene Tree for LRIT3 (if available)

Paralogs for LRIT3 Gene

Paralogs for LRIT3 Gene

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

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

Variants for LRIT3 Gene

Sequence variations from dbSNP and Humsavar for LRIT3 Gene

SNP ID Clin Chr 04 pos Variation AA Info Type
rs10011256 likely-benign, Congenital Stationary Night Blindness, Recessive 109,871,751(+) A/G 3_prime_UTR_variant, genic_downstream_transcript_variant
rs1032235214 uncertain-significance, Congenital Stationary Night Blindness, Recessive 109,872,305(+) C/A 3_prime_UTR_variant, genic_downstream_transcript_variant
rs116151046 uncertain-significance, Congenital Stationary Night Blindness, Recessive 109,871,021(+) C/G 3_prime_UTR_variant, downstream_transcript_variant, genic_downstream_transcript_variant
rs12642452 benign, Congenital Stationary Night Blindness, Recessive 109,871,912(+) T/C 3_prime_UTR_variant, genic_downstream_transcript_variant
rs139529995 uncertain-significance, Congenital Stationary Night Blindness, Recessive 109,871,178(+) G/A 3_prime_UTR_variant, downstream_transcript_variant, genic_downstream_transcript_variant

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)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

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

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

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


  • 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}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for LRIT3

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with LRIT3: view

No data available for Genatlas for LRIT3 Gene

Publications for LRIT3 Gene

  1. 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 58
  2. 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 58
  3. 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 44 58
  4. 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 58
  5. 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 58

Products for LRIT3 Gene

Sources for LRIT3 Gene

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