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    IGSF21 immunoglobin superfamily member 21 [ Homo sapiens (human) ]

    Gene ID: 84966, updated on 5-Mar-2024

    Summary

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    Official Symbol
    IGSF21provided by HGNC
    Official Full Name
    immunoglobin superfamily member 21provided by HGNC
    Primary source
    HGNC:HGNC:28246
    See related
    Ensembl:ENSG00000117154 AllianceGenome:HGNC:28246
    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
    Summary
    This gene encodes a protein which has two immunoglobulin (Ig) domains and is a member of the immunoglobulin superfamily. Proteins in this superfamily are usually found on or in cell membranes and act as receptors in immune response pathways. [provided by RefSeq, Sep 2011]
    Expression
    Biased expression in brain (RPKM 11.7), spleen (RPKM 6.4) and 6 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See IGSF21 in Genome Data Viewer
    Location:
    1p36.13
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (18107798..18378483)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (17927918..18198544)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (18434292..18704977)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105376812 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:18404738-18404927 Neighboring gene long intergenic non-protein coding RNA 1654 Neighboring gene Sharpr-MPRA regulatory region 487 Neighboring gene NANOG hESC enhancer GRCh37_chr1:18425418-18425940 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:18468715-18469332 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:18469333-18469948 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:18473111-18473612 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:18473613-18474112 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:18482493-18483371 Neighboring gene IGSF21 antisense RNA 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:18501697-18502198 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:18502199-18502698 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:18525748-18526248 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:18526249-18526749 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:18527418-18527918 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:18538061-18538884 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:18557491-18558139 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:18575476-18575976 Neighboring gene uncharacterized LOC124903864 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:18606867-18607381 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:18607382-18607895 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:18609585-18610784 Neighboring gene uncharacterized LOC124903863 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:18620236-18621123 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:18622899-18623785 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:18624079-18624604 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:18626609-18627236 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:18633258-18633415 Neighboring gene Sharpr-MPRA regulatory region 11488 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:18672835-18673336 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:18673337-18673836 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:18709612-18710411 Neighboring gene uncharacterized LOC124903865 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:18733166-18733860 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:18733861-18734554 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:18794765-18794938 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:18806502-18807374 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:18807375-18808246 Neighboring gene kelch domain containing 7A

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. Association between LEKR1-CCNL1 and IGSF21-KLHDC7A gene polymorphisms and diabetic retinopathy of type 2 diabetes mellitus in the Chinese Han population. Lin X, et al. J Gene Med, 2016 Oct. PMID 27607899
    2. IgSF21 promotes differentiation of inhibitory synapses via binding to neurexin2α. Tanabe Y, et al. Nat Commun, 2017 Sep 1. PMID 28864826, Free PMC Article
    3. Genome-wide association study to identify single nucleotide polymorphisms (SNPs) associated with the development of erectile dysfunction in African-American men after radiotherapy for prostate cancer. Kerns SL, et al. Int J Radiat Oncol Biol Phys, 2010 Dec 1. PMID 20932654, Free PMC Article
    4. Genome-wide meta-analysis for severe diabetic retinopathy. Grassi MA, et al. Hum Mol Genet, 2011 Jun 15. PMID 21441570, Free PMC Article
    5. Coeliac disease-associated risk variants in TNFAIP3 and REL implicate altered NF-kappaB signalling. Trynka G, et al. Gut, 2009 Aug. PMID 19240061

    See all (15) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Results suggest that LEKR1-CCNL1 and IGSF21-KLHDC7A gene polymorphisms influence the development of diabetic retinopathy (DR).
      Title: Association between LEKR1-CCNL1 and IGSF21-KLHDC7A gene polymorphisms and diabetic retinopathy of type 2 diabetes mellitus in the Chinese Han population.
    2. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    3. Observational study of gene-disease association. (HuGE Navigator)
      Title: Coeliac disease-associated risk variants in TNFAIP3 and REL implicate altered NF-kappaB signalling.
    Submit: New GeneRIF Correction

    Phenotypes

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

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genome-wide association study to identify single nucleotide polymorphisms (SNPs) associated with the development of erectile dysfunction in African-American men after radiotherapy for prostate cancer.
    EBI GWAS Catalog
    Genome-wide meta-analysis for severe diabetic retinopathy.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ41177, MGC15730

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in homophilic cell adhesion via plasma membrane adhesion molecules IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in synapse maturation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    is_active_in adherens junction IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in external side of plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in inhibitory synapse ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in postsynaptic membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in presynaptic membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    immunoglobulin superfamily member 21

    NCBI Reference Sequences (RefSeq)

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    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_027535.2 RefSeqGene

      Range
      5053..275738
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_032880.5 → NP_116269.3  immunoglobulin superfamily member 21 precursor

      See identical proteins and their annotated locations for NP_116269.3

      Status: REVIEWED

      Source sequence(s)
      AK075316, AL356101, BC007618
      Consensus CDS
      CCDS184.1
      UniProtKB/Swiss-Prot
      Q8NBR8, Q96ID5
      Related
      ENSP00000251296.1, ENST00000251296.4
      Conserved Domains (2) summary
      smart00410
      Location:353 → 430
      IG_like; Immunoglobulin like
      cl11960
      Location:369 → 432
      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
      18107798..18378483
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011542319.4 → XP_011540621.1  immunoglobulin superfamily member 21 isoform X3

      Conserved Domains (2) summary
      smart00410
      Location:156 → 233
      IG_like; Immunoglobulin like
      cl11960
      Location:172 → 235
      Ig; Immunoglobulin domain

    2. XM_017002604.3 → XP_016858093.1  immunoglobulin superfamily member 21 isoform X1

      Conserved Domains (2) summary
      smart00410
      Location:347 → 424
      IG_like; Immunoglobulin like
      cl11960
      Location:363 → 426
      Ig; Immunoglobulin domain

    3. XM_017002605.1 → XP_016858094.1  immunoglobulin superfamily member 21 isoform X2

      Conserved Domains (2) summary
      smart00410
      Location:276 → 353
      IG_like; Immunoglobulin like
      cl11960
      Location:292 → 355
      Ig; Immunoglobulin domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      17927918..18198544
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054339280.1 → XP_054195255.1  immunoglobulin superfamily member 21 isoform X3

    2. XM_054339278.1 → XP_054195253.1  immunoglobulin superfamily member 21 isoform X1

    3. XM_054339279.1 → XP_054195254.1  immunoglobulin superfamily member 21 isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96ID5.1 GenPept UniProtKB/Swiss-Prot:Q96ID5

    Gene LinkOut

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

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