Free for academic non-profit institutions. Other users need a Commercial license

Aliases for IGSF3 Gene

Aliases for IGSF3 Gene

  • Immunoglobulin Superfamily Member 3 2 3 5
  • Glu-Trp-Ile EWI Motif-Containing Protein 3 3 4
  • EWI-3 3 4
  • Immunoglobulin Superfamily, Member 3 2
  • Immunoglobin Superfamily, Member 3 3
  • KIAA0466 4
  • IgSF3 4
  • LCDD 3
  • EWI3 4
  • V8 3

External Ids for IGSF3 Gene

Previous GeneCards Identifiers for IGSF3 Gene

  • GC01M117619
  • GC01M115999
  • GC01M116264
  • GC01M116466
  • GC01M116829
  • GC01M116918
  • GC01M117117
  • GC01M114976

Summaries for IGSF3 Gene

Entrez Gene Summary for IGSF3 Gene

  • The protein encoded by this gene is an immunoglobulin-like membrane protein containing several V-type Ig-like domains. A mutation in this gene has been associated with bilateral nasolacrimal duct obstruction (LCDD). [provided by RefSeq, Jun 2016]

GeneCards Summary for IGSF3 Gene

IGSF3 (Immunoglobulin Superfamily Member 3) is a Protein Coding gene. Diseases associated with IGSF3 include Lacrimal Duct Defect. An important paralog of this gene is CD101.

Additional gene information for IGSF3 Gene

No data available for CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for IGSF3 Gene

Genomics for IGSF3 Gene

Regulatory Elements for IGSF3 Gene

Enhancers for IGSF3 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH01H116645 1.1 Ensembl ENCODE 30.4 +20.1 20083 3 HDGF FOXA2 SIN3A KLF17 FEZF1 YY1 FOS ATF7 ZEB2 ZNF217 IGSF3 MIR320B1 C1orf137 CD101 LOC105378924
GH01H116693 1 ENCODE dbSUPER 22.2 -26.6 -26578 1 BCOR TBP PTBP1 ZMYM3 SMC3 RCOR1 FOS NFE2 NFE2L2 SMARCA5 IGSF3 MIR320B1 CD2 C1orf137 LOC105378926
GH01H116678 1.2 ENCODE dbSUPER 15.3 -12.0 -11967 2 HDGF ATF1 ARNT YY1 TCF12 GTF3C2 ZNF766 GATA2 CAVIN1 ZNF592 ATP1A1-AS1 IGSF3 MAN1A2 MIR320B1 C1orf137
GH01H116823 1.6 Ensembl ENCODE dbSUPER 10.7 -158.4 -158444 4 HDGF PKNOX1 ARNT FEZF1 ZNF2 ZNF766 ZNF143 ZNF207 FOS JUNB ENSG00000237993 MAN1A2 ATP1A1-AS1 NEFHP1 LINC01525 VPS25P1 IGSF3 CD2 PTGFRN MIR320B1
GH01H116880 1.6 FANTOM5 Ensembl ENCODE 10.6 -214.1 -214052 2 HDGF PKNOX1 ATF1 ARNT TCF12 ZNF766 GATA2 ZNF143 FOS ATF7 PTGFRN IGSF3 MIR320B1 CD101 LOC105378927 FTH1P22
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around IGSF3 on UCSC Golden Path with GeneCards custom track

Promoters for IGSF3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000011960 155 1201 HDAC1 TBP RB1 SIN3A ZBTB40 GLIS2 GATA2 RCOR1 CREM IKZF2

Genomic Location for IGSF3 Gene

Chromosome:
1
Start:
116,574,398 bp from pter
End:
116,667,755 bp from pter
Size:
93,358 bases
Orientation:
Minus strand

Genomic View for IGSF3 Gene

Genes around IGSF3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
IGSF3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for IGSF3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for IGSF3 Gene

Proteins for IGSF3 Gene

  • Protein details for IGSF3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O75054-IGSF3_HUMAN
    Recommended name:
    Immunoglobulin superfamily member 3
    Protein Accession:
    O75054
    Secondary Accessions:
    • A6NJZ6
    • A6NMC7

    Protein attributes for IGSF3 Gene

    Size:
    1194 amino acids
    Molecular mass:
    135196 Da
    Quaternary structure:
    No Data Available
    Miscellaneous:
    • Likely interchromosomal Alu-mediated fusion between IGSF3 on 1p13.1 and GGT on 22q11.2. Breakpoints occurred inside Alu elements as well as in the 5 or 3 ends of them.
    SequenceCaution:
    • Sequence=AAC72013.1; Type=Frameshift; Positions=829, 861; Evidence={ECO:0000305}; Sequence=BAA32311.2; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Alternative splice isoforms for IGSF3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for IGSF3 Gene

Post-translational modifications for IGSF3 Gene

  • Glycosylation at posLast=4343, isoforms=2418, isoforms=2655, posLast=842842, isoforms=2961, and posLast=10771077
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for IGSF3 Gene

Domains & Families for IGSF3 Gene

Gene Families for IGSF3 Gene

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

Suggested Antigen Peptide Sequences for IGSF3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with IGSF3: view

No data available for UniProtKB/Swiss-Prot for IGSF3 Gene

Function for IGSF3 Gene

Molecular function for IGSF3 Gene

GENATLAS Biochemistry:
immunoglobulin superfamily member 3,highly expressed in placenta,kidney and lung

Phenotypes From GWAS Catalog for IGSF3 Gene

Gene Ontology (GO) - Molecular Function for IGSF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
genes like me logo Genes that share ontologies with IGSF3: view
genes like me logo Genes that share phenotypes with IGSF3: view

Human Phenotype Ontology for IGSF3 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for IGSF3
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for IGSF3 Gene

Localization for IGSF3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for IGSF3 Gene

Membrane; Single-pass type I membrane protein.

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 IGSF3 gene
Compartment Confidence
plasma membrane 5
extracellular 2
nucleus 2
cytosol 2
endoplasmic reticulum 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

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

Gene Ontology (GO) - Cellular Components for IGSF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IBA --
GO:0009986 cell surface IDA 19581412
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IBA --
genes like me logo Genes that share ontologies with IGSF3: view

Pathways & Interactions for IGSF3 Gene

SuperPathways for IGSF3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for IGSF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007166 cell surface receptor signaling pathway IBA --
GO:0032808 lacrimal gland development IMP 24372406
genes like me logo Genes that share ontologies with IGSF3: view

No data available for Pathways by source and SIGNOR curated interactions for IGSF3 Gene

Drugs & Compounds for IGSF3 Gene

No Compound Related Data Available

Transcripts for IGSF3 Gene

Unigene Clusters for IGSF3 Gene

Immunoglobulin superfamily, member 3:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for IGSF3
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

Alternative Splicing Database (ASD) splice patterns (SP) for IGSF3 Gene

No ASD Table

Relevant External Links for IGSF3 Gene

GeneLoc Exon Structure for
IGSF3
ECgene alternative splicing isoforms for
IGSF3

Expression for IGSF3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for IGSF3 Gene

mRNA differential expression in normal tissues according to GTEx for IGSF3 Gene

This gene is overexpressed in Esophagus - Mucosa (x5.5).

Protein differential expression in normal tissues from HIPED for IGSF3 Gene

This gene is overexpressed in Fetal Brain (55.3) and Placenta (6.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for IGSF3 Gene



NURSA nuclear receptor signaling pathways regulating expression of IGSF3 Gene:

IGSF3

SOURCE GeneReport for Unigene cluster for IGSF3 Gene:

Hs.171057

mRNA Expression by UniProt/SwissProt for IGSF3 Gene:

O75054-IGSF3_HUMAN
Tissue specificity: Expressed in a wide range of tissues with High expression in Placenta, kidney and lung.

Evidence on tissue expression from TISSUES for IGSF3 Gene

  • Nervous system(4.5)
  • Skin(2.6)
  • Kidney(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for IGSF3 Gene

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • integumentary
  • nervous
Organs:
Head and neck:
  • head
  • lacrimal apparatus
genes like me logo Genes that share expression patterns with IGSF3: view

Primer Products

No data available for Protein tissue co-expression partners for IGSF3 Gene

Orthologs for IGSF3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for IGSF3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia IGSF3 33 34
  • 99.04 (n)
dog
(Canis familiaris)
Mammalia IGSF3 33 34
  • 89.87 (n)
cow
(Bos Taurus)
Mammalia IGSF3 33 34
  • 88.19 (n)
mouse
(Mus musculus)
Mammalia Igsf3 33 16 34
  • 87.72 (n)
rat
(Rattus norvegicus)
Mammalia Igsf3 33
  • 87.41 (n)
oppossum
(Monodelphis domestica)
Mammalia IGSF3 34
  • 79 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia IGSF3 34
  • 55 (a)
OneToOne
chicken
(Gallus gallus)
Aves IGSF3 33 34
  • 75.87 (n)
lizard
(Anolis carolinensis)
Reptilia IGSF3 34
  • 68 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia igsf3 33
  • 62.79 (n)
Str.5486 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.16592 33
zebrafish
(Danio rerio)
Actinopterygii si:ch211-247j6.1 33
  • 58.79 (n)
IGSF3 34
  • 54 (a)
OneToOne
Species where no ortholog for IGSF3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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 IGSF3 Gene

ENSEMBL:
Gene Tree for IGSF3 (if available)
TreeFam:
Gene Tree for IGSF3 (if available)

Paralogs for IGSF3 Gene

Paralogs for IGSF3 Gene

(3) SIMAP similar genes for IGSF3 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with IGSF3: view

Variants for IGSF3 Gene

Sequence variations from dbSNP and Humsavar for IGSF3 Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type
rs724160030 Pathogenic 116,579,791(-) TGTCC(-/C)GCTCC reference, frameshift-variant
rs1000035330 -- 116,587,196(+) AGAGA(C/T)AGAAA intron-variant, upstream-variant-2KB
rs1000052371 -- 116,630,118(+) AATGG(C/G)ATTTG intron-variant
rs1000308253 -- 116,574,831(+) CGCAT(G/T)TCCAT utr-variant-3-prime
rs1000353789 -- 116,663,721(+) TTGAG(A/G)GAGAT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for IGSF3 Gene

Variant ID Type Subtype PubMed ID
dgv85e212 CNV loss 25503493
esv2758963 CNV gain+loss 17122850
esv28283 CNV gain+loss 19812545
esv32882 CNV gain 17666407
esv33190 CNV gain+loss 17666407
esv3578131 CNV loss 25503493
nsv10661 CNV gain+loss 18304495
nsv1116609 CNV tandem duplication 24896259
nsv428190 CNV gain 18775914
nsv482103 CNV gain 20164927
nsv824309 CNV gain 20364138
nsv831148 CNV gain 17160897
nsv945587 CNV duplication 23825009
nsv945588 CNV duplication 23825009
nsv946165 CNV duplication 23825009
nsv946166 CNV duplication 23825009
nsv946167 CNV duplication 23825009
nsv946168 CNV duplication 23825009

Variation tolerance for IGSF3 Gene

Residual Variation Intolerance Score: 61.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 10.32; 90.70% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for IGSF3 Gene

Human Gene Mutation Database (HGMD)
IGSF3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
IGSF3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for IGSF3 Gene

Disorders for IGSF3 Gene

MalaCards: The human disease database

(1) MalaCards diseases for IGSF3 Gene - From: HGMD, OMIM, ClinVar, Orphanet, and GeneCards

Disorder Aliases PubMed IDs
lacrimal duct defect
  • lacrimal duct obstruction
- elite association - COSMIC cancer census association via MalaCards
Search IGSF3 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

IGSF3_HUMAN
  • Lacrimal duct defect (LCDD) [MIM:149700]: A condition resulting in the imbalance between tear production and tear drainage. Infants typically manifest persistent epiphora and/or recurrent infections of the lacrimal pathway, such as conjunctivitis. LCDD is caused by failure of the nasolacrimal duct to open into the inferior meatus. {ECO:0000269 PubMed:24372406}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for IGSF3

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
IGSF3
genes like me logo Genes that share disorders with IGSF3: view

No data available for Genatlas for IGSF3 Gene

Publications for IGSF3 Gene

  1. Molecular cloning of a human cDNA IGSF3 encoding an immunoglobulin-like membrane protein: expression and mapping to chromosome band 1p13. (PMID: 9790749) Saupe S … De Sario A (Genomics 1998) 2 3 4 60
  2. Identification of an IGSF3 mutation in a family with congenital nasolacrimal duct obstruction. (PMID: 24372406) Foster J … Tekin M (Clinical genetics 2014) 3 4 60
  3. EWI-2 is a major CD9 and CD81 partner and member of a novel Ig protein subfamily. (PMID: 11504738) Stipp CS … Hemler ME (The Journal of biological chemistry 2001) 4 22 60
  4. Characterization of cDNA clones in size-fractionated cDNA libraries from human brain. (PMID: 9455484) Seki N … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 1997) 3 4 60
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 60

Products for IGSF3 Gene

Sources for IGSF3 Gene

Content
Loading form....