U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

IGSF3 immunoglobulin superfamily member 3 [ Homo sapiens (human) ]

Gene ID: 3321, updated on 11-Apr-2024

Summary

Go to the top of the page Help
Official Symbol
IGSF3provided by HGNC
Official Full Name
immunoglobulin superfamily member 3provided by HGNC
Primary source
HGNC:HGNC:5950
See related
Ensembl:ENSG00000143061 MIM:603491; AllianceGenome:HGNC:5950
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
V8; LCDD; EWI-3
Summary
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]
Expression
Broad expression in esophagus (RPKM 8.2), skin (RPKM 7.8) and 19 other tissues See more
Orthologs
mouse all
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See IGSF3 in Genome Data Viewer
Location:
1p13.1
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (116574398..116667755, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (116584842..116678201, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (117117020..117210377, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene CD58 molecule Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1565 Neighboring gene nucleosome assembly protein 1 like 4 pseudogene 1 Neighboring gene uncharacterized LOC105378925 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1566 Neighboring gene Sharpr-MPRA regulatory region 4262 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1568 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1569 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1570 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1571 Neighboring gene microRNA 548ac Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1232 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1233 Neighboring gene uncharacterized LOC124904385 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1572 Neighboring gene uncharacterized LOC105378924 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1234 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:117142207-117142708 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:117150835-117151334 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:117156699-117157269 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:117161725-117162232 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr1:117184821-117185506 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:117185507-117186190 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:117188080-117188811 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:117188812-117189542 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:117189543-117190273 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1235 Neighboring gene microRNA 320b-1 Neighboring gene CRISPRi-validated cis-regulatory element chr1.8052 Neighboring gene long intergenic non-protein coding RNA 2868 Neighboring gene uncharacterized LOC105378926

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

Go to the top of the pageHelp

Related articles in PubMed

  1. IGSF3 mutation identified in patient with severe COPD alters cell function and motility. Schweitzer KS, et al. JCI Insight, 2020 Jul 23. PMID 32573489, Free PMC Article
  2. Molecular cloning of a human cDNA IGSF3 encoding an immunoglobulin-like membrane protein: expression and mapping to chromosome band 1p13. Saupe S, et al. Genomics, 1998 Sep 15. PMID 9790749
  3. Osteoclastogenesis inhibition by mutated IGSF23 results in human osteopetrosis. Yuan Y, et al. Cell Prolif, 2019 Nov. PMID 31560140, Free PMC Article
  4. Identification of an IGSF3 mutation in a family with congenital nasolacrimal duct obstruction. Foster J 2nd, et al. Clin Genet, 2014 Dec. PMID 24372406
  5. Rank-based genome-wide analysis reveals the association of ryanodine receptor-2 gene variants with childhood asthma among human populations. Ding L, et al. Hum Genomics, 2013 Jul 5. PMID 23829686, Free PMC Article

See all (28) citations in PubMed

GeneRIFs: Gene References Into Functions

Phenotypes

Go to the top of the page Help

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Familial congenital nasolacrimal duct obstruction
MedGen: C1835612 OMIM: 149700 GeneReviews: Not available
Compare labs

EBI GWAS Catalog

Description
Rank-based genome-wide analysis reveals the association of ryanodine receptor-2 gene variants with childhood asthma among human populations.
EBI GWAS Catalog

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

Markers

Homology

Clone Names

  • MGC117164

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables molecular_function ND
No biological Data available
more info
  
Process Evidence Code Pubs
involved_in lacrimal gland development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in cell surface HDA PubMed 
is_active_in membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

Go to the top of the page Help
Preferred Names
immunoglobulin superfamily member 3
Names
glu-Trp-Ile EWI motif-containing protein 3
immunoglobin superfamily, member 3

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_050917.1 RefSeqGene

    Range
    5023..98348
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001007237.3 → NP_001007238.1  immunoglobulin superfamily member 3 isoform 2 precursor

    See identical proteins and their annotated locations for NP_001007238.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and lacks an alternate in-frame exon, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AB007935, AI968231, BC110651
    Consensus CDS
    CCDS30813.1
    UniProtKB/Swiss-Prot
    A6NJZ6, A6NMC7, O75054
    Related
    ENSP00000358498.4, ENST00000369486.8
    Conserved Domains (6) summary
    smart00409
    Location:293 → 389
    IG; Immunoglobulin
    pfam07686
    Location:687 → 784
    V-set; Immunoglobulin V-set domain
    pfam13927
    Location:410 → 514
    Ig_3; Immunoglobulin domain
    cd00096
    Location:689 → 692
    Ig; Ig strand A' [structural motif]
    cd00099
    Location:152 → 251
    IgV; Immunoglobulin variable domain (IgV)
    cl11960
    Location:821 → 920
    Ig; Immunoglobulin domain

  2. NM_001542.4 → NP_001533.2  immunoglobulin superfamily member 3 isoform 1 precursor

    See identical proteins and their annotated locations for NP_001533.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AB007935, AF031174, AI968231, BC110651
    Consensus CDS
    CCDS30814.1
    UniProtKB/Swiss-Prot
    O75054
    Related
    ENSP00000358495.1, ENST00000369483.5
    Conserved Domains (4) summary
    smart00406
    Location:163 → 247
    IGv; Immunoglobulin V-Type
    smart00410
    Location:707 → 830
    IG_like; Immunoglobulin like
    pfam07686
    Location:707 → 830
    V-set; Immunoglobulin V-set domain
    cl11960
    Location:34 → 141
    Ig; Immunoglobulin domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    116574398..116667755 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047419052.1 → XP_047275008.1  immunoglobulin superfamily member 3 isoform X3

  2. XM_047419070.1 → XP_047275026.1  immunoglobulin superfamily member 3 isoform X5

    UniProtKB/Swiss-Prot
    A6NJZ6, A6NMC7, O75054

  3. XM_047419042.1 → XP_047274998.1  immunoglobulin superfamily member 3 isoform X3

  4. XM_011541315.2 → XP_011539617.1  immunoglobulin superfamily member 3 isoform X2

    See identical proteins and their annotated locations for XP_011539617.1

    UniProtKB/Swiss-Prot
    O75054
    Related
    ENSP00000321184.6, ENST00000318837.6
    Conserved Domains (4) summary
    smart00406
    Location:163 → 247
    IGv; Immunoglobulin V-Type
    smart00410
    Location:707 → 830
    IG_like; Immunoglobulin like
    pfam07686
    Location:707 → 830
    V-set; Immunoglobulin V-set domain
    cl11960
    Location:34 → 141
    Ig; Immunoglobulin domain

  5. XM_006710593.4 → XP_006710656.1  immunoglobulin superfamily member 3 isoform X1

    Conserved Domains (4) summary
    smart00406
    Location:168 → 252
    IGv; Immunoglobulin V-Type
    smart00410
    Location:712 → 835
    IG_like; Immunoglobulin like
    pfam07686
    Location:712 → 835
    V-set; Immunoglobulin V-set domain
    cl11960
    Location:39 → 146
    Ig; Immunoglobulin domain

  6. XM_005270794.5 → XP_005270851.1  immunoglobulin superfamily member 3 isoform X4

    Conserved Domains (4) summary
    smart00406
    Location:168 → 252
    IGv; Immunoglobulin V-Type
    smart00410
    Location:692 → 815
    IG_like; Immunoglobulin like
    pfam07686
    Location:692 → 815
    V-set; Immunoglobulin V-set domain
    cl11960
    Location:39 → 146
    Ig; Immunoglobulin domain

  7. XM_011541316.3 → XP_011539618.1  immunoglobulin superfamily member 3 isoform X6

    Conserved Domains (3) summary
    smart00410
    Location:150 → 273
    IG_like; Immunoglobulin like
    pfam07686
    Location:150 → 273
    V-set; Immunoglobulin V-set domain
    cl11960
    Location:284 → 395
    Ig; Immunoglobulin domain

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    116584842..116678201 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054336231.1 → XP_054192206.1  immunoglobulin superfamily member 3 isoform X3

  2. XM_054336229.1 → XP_054192204.1  immunoglobulin superfamily member 3 isoform X2

  3. XM_054336233.1 → XP_054192208.1  immunoglobulin superfamily member 3 isoform X5

  4. XM_054336230.1 → XP_054192205.1  immunoglobulin superfamily member 3 isoform X3

  5. XM_054336228.1 → XP_054192203.1  immunoglobulin superfamily member 3 isoform X1

  6. XM_054336232.1 → XP_054192207.1  immunoglobulin superfamily member 3 isoform X4

  7. XM_054336234.1 → XP_054192209.1  immunoglobulin superfamily member 3 isoform X6

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O75054.3 GenPept UniProtKB/Swiss-Prot:O75054

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information
Molecular Biology Databases
Research Materials
Tools
Miscellaneous