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] See more...

Aliases for IGSF3 Gene

Aliases for IGSF3 Gene

  • Immunoglobulin Superfamily Member 3 2 3 4 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 Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for IGSF3 Gene

Genomics for IGSF3 Gene

GeneHancer (GH) Regulatory Elements for IGSF3 Gene

Promoters and enhancers for IGSF3 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
GH01J116666 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE CraniofacialAtlas 750.6 +0.9 854 3 ZBTB40 GATA3 SMARCE1 ZNF217 L3MBTL2 MNT POLR2A ZFX SP7 ZNF687 IGSF3 RF01045-010
GH01J116645 Promoter/Enhancer 1.3 Ensembl ENCODE CraniofacialAtlas 30.4 +20.2 20185 4 FOXA1 MNT SP1 CEBPG ZSCAN21 PRDM1 ZIC2 CEBPA RXRA ZEB2 IGSF3 MIR320B1 C1orf137 CD101 RF01045-010
GH01J116693 Enhancer 1.3 Ensembl ENCODE CraniofacialAtlas dbSUPER 22.2 -27.8 -27846 6 ZNF362 ZNF148 MLLT1 IKZF1 PKNOX1 SMARCC1 ZSCAN4 POLR2A ZNF316 ZNF24 C1orf137 IGSF3 ATP1A1-AS1 MIR320B1 CD2 LOC105378926
GH01J116678 Enhancer 1.4 Ensembl ENCODE CraniofacialAtlas dbSUPER 15.3 -12.4 -12433 3.9 GTF3C2 ZBTB40 SMARCE1 RUNX1 CC2D1A RBM39 L3MBTL2 TEAD4 ZKSCAN8 ZNF148 ATP1A1-AS1 CD2 IGSF3 CD58 MAN1A2 MIR320B1 C1orf137
GH01J116823 Enhancer 1.5 Ensembl ENCODE CraniofacialAtlas dbSUPER 10.7 -158.4 -158443 4.9 SP1 ZBTB40 CTCF SMARCE1 JUND CC2D1A ETV6 ELF1 RELA RBM39 ATP1A1-AS1 ENSG00000237993 MAN1A2 NEFHP1 LINC01525 VPS25P1 IGSF3 CD2 PTGFRN MIR320B1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around IGSF3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the IGSF3 gene promoter:
  • AML1a
  • Arnt
  • HOXA9
  • HOXA9B
  • Ik-1
  • Meis-1
  • Meis-1b
  • PPAR-gamma1
  • PPAR-gamma2

Genomic Locations for IGSF3 Gene

Genomic Locations for IGSF3 Gene
chr1:116,574,398-116,667,755
(GRCh38/hg38)
Size:
93,358 bases
Orientation:
Minus strand
chr1:117,117,031-117,210,375
(GRCh37/hg19)
Size:
93,345 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 Asn43, Asn418, Asn655, Asn700, Asn842, Asn961, and Asn1077
  • Modification sites at PhosphoSitePlus
  • Glycosylation from GlyConnect
    • IGSF3_HUMAN (1392)

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:
  • Glu-Trp-Ile EWI motif-containing protein 3 (IGSF3_HUMAN)
genes like me logo Genes that share domains with IGSF3: view

No data available for Graphical View of Domain Structure and 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

Clone Products

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 3
extracellular 2
nucleus 2
endoplasmic reticulum 1
cytosol 1
lysosome 0
golgi apparatus 0

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:0009986 cell surface HDA 19581412
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IBA 21873635
genes like me logo Genes that share ontologies with IGSF3: view

Pathways & Interactions for IGSF3 Gene

PathCards logo

SuperPathways for IGSF3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for IGSF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
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

mRNA/cDNA for IGSF3 Gene

CRISPR Products

Clone Products

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, 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(2.1)

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

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

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 32
  • 99.04 (n)
OneToOne
dog
(Canis familiaris)
Mammalia IGSF3 33 32
  • 89.87 (n)
OneToOne
cow
(Bos Taurus)
Mammalia IGSF3 33 32
  • 88.19 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Igsf3 17 33 32
  • 87.72 (n)
rat
(Rattus norvegicus)
Mammalia Igsf3 32
  • 87.41 (n)
oppossum
(Monodelphis domestica)
Mammalia IGSF3 33
  • 79 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia IGSF3 33
  • 55 (a)
OneToOne
chicken
(Gallus gallus)
Aves IGSF3 33 32
  • 75.87 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia IGSF3 33
  • 68 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia igsf3 32
  • 62.79 (n)
Str.5486 32
African clawed frog
(Xenopus laevis)
Amphibia Xl.16592 32
zebrafish
(Danio rerio)
Actinopterygii si:ch211-247j6.1 32
  • 58.79 (n)
IGSF3 33
  • 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)
Aminode:
Evolutionary constrained regions (ECRs) for IGSF3: view image

Paralogs for IGSF3 Gene

Paralogs for IGSF3 Gene

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

  • IGSF3_HUMAN
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 Variation AA Info Type
rs724160030 pathogenic, Lacrimal duct defect 116,579,791(-) GGG/GG coding_sequence_variant, frameshift
rs200735353 uncertain-significance, not provided 116,600,223(-) G/A coding_sequence_variant, missense_variant
rs41301291 benign, not specified 116,584,795(-) C/T coding_sequence_variant, missense_variant
rs1000035330 -- 116,587,196(-) T/C intron_variant
rs1000052371 -- 116,630,118(-) G/C genic_upstream_transcript_variant, 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)

Additional Variant Information for IGSF3 Gene

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

SNP Genotyping and Copy Number Assay Products

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, GTR, Orphanet, and GeneCards

Disorder Aliases PubMed IDs
lacrimal duct defect
  • lcdd
- 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.

Additional Disease Information for 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 56
  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 56
  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 23 56
  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 56
  5. The Functional Proximal Proteome of Oncogenic Ras Includes mTORC2. (PMID: 30639242) Kovalski JR … Khavari PA (Molecular cell 2019) 3 56

Products for IGSF3 Gene

Sources for IGSF3 Gene