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    KIRREL3 kirre like nephrin family adhesion molecule 3 [ Homo sapiens (human) ]

    Gene ID: 84623, updated on 12-Aug-2018

    Summary

    Official Symbol
    KIRREL3provided by HGNC
    Official Full Name
    kirre like nephrin family adhesion molecule 3provided by HGNC
    Primary source
    HGNC:HGNC:23204
    See related
    Ensembl:ENSG00000149571 MIM:607761; Vega:OTTHUMG00000165831
    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
    MRD4; KIRRE; NEPH2; PRO4502
    Summary
    The protein encoded by this gene is a member of the nephrin-like protein family. These proteins are expressed in fetal and adult brain, and also in podocytes of kidney glomeruli. The cytoplasmic domains of these proteins interact with the C-terminus of podocin, also expressed in the podocytes, cells involved in ensuring size- and charge-selective ultrafiltration. The protein encoded by this gene is a synaptic cell adhesion molecule with multiple extracellular immunoglobulin-like domains and a cytoplasmic PDZ domain-binding motif. Mutations in this gene are associated with several neurological and cognitive disorders. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2017]
    Expression
    Biased expression in brain (RPKM 6.0), adrenal (RPKM 0.5) and 1 other tissue See more
    Orthologs

    Genomic context

    See KIRREL3 in Genome Data Viewer
    Location:
    11q24.2
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    109 current GRCh38.p12 (GCF_000001405.38) 11 NC_000011.10 (126423493..127003460, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (126293388..126870766, complement)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene decapping enzyme, scavenger Neighboring gene ST3 beta-galactoside alpha-2,3-sialyltransferase 4 Neighboring gene G-quadruplex forming sequence containing lncRNA Neighboring gene uncharacterized LOC101929427 Neighboring gene uncharacterized LOC105369561 Neighboring gene uncharacterized LOC105369559 Neighboring gene KIRREL3 antisense RNA 2 Neighboring gene uncharacterized LOC105369558 Neighboring gene KIRREL3 antisense RNA 3 Neighboring gene microRNA 3167 Neighboring gene uncharacterized LOC101929473 Neighboring gene uncharacterized LOC105369562

    Genomic regions, transcripts, and products

    Expression

    • 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 Jun 15 11:32:44 2016

    Bibliography

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Mental retardation, autosomal dominant 4
    MedGen: C2675487 OMIM: 612581 GeneReviews: Not available
    Compare labs

    NHGRI GWAS Catalog

    Description
    A genome-wide association study identifies protein quantitative trait loci (pQTLs).
    NHGRI GWA Catalog
    Conduct disorder and ADHD: evaluation of conduct problems as a categorical and quantitative trait in the international multicentre ADHD genetics study.
    NHGRI GWA Catalog
    Genetic variants associated with breast size also influence breast cancer risk.
    NHGRI GWA Catalog
    Genome wide association study of age at menarche in the Japanese population.
    NHGRI GWA Catalog
    Genomewide pharmacogenomic study of metabolic side effects to antipsychotic drugs.
    NHGRI GWA Catalog
    Web-based, participant-driven studies yield novel genetic associations for common traits.
    NHGRI GWA Catalog

    Pathways from BioSystems

    • Cell-Cell communication, organism-specific biosystem (from REACTOME)
      Cell-Cell communication, organism-specific biosystemCell-to-Cell communication is crucial for multicellular organisms because it allows organisms to coordinate the activity of their cells. Some cell-to-cell communication requires direct cell-cell cont...
    • Nephrin interactions, organism-specific biosystem (from REACTOME)
      Nephrin interactions, organism-specific biosystemNephrin is a member of the Super-IgG-Molecule family and is most prominently expressed in kidney podocytes. It is a major if not the most important structural component of the slit diaphragm, a modif...
    • Primary Focal Segmental Glomerulosclerosis FSGS, organism-specific biosystem (from WikiPathways)
      Primary Focal Segmental Glomerulosclerosis FSGS, organism-specific biosystemPrimary or idiopathic focal segmental glomerulosclerosis (FSGS) a cause of nephrotic syndrome in children and adolescents, as well as an important cause of end stage renal disease in adults. FSGS is ...

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • KIAA1867, MGC126824, MGC126850

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    glomerulus morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    hemopoiesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    hippocampus development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    homophilic cell adhesion via plasma membrane adhesion molecules ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    inter-male aggressive behavior IEA
    Inferred from Electronic Annotation
    more info
     
    neuron migration IEA
    Inferred from Electronic Annotation
    more info
     
    neuron projection morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    principal sensory nucleus of trigeminal nerve development IEA
    Inferred from Electronic Annotation
    more info
     
    synapse assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Component Evidence Code Pubs
    axon ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    dendrite ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    dendritic shaft IEA
    Inferred from Electronic Annotation
    more info
     
    extracellular region ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    integral component of membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    plasma membrane TAS
    Traceable Author Statement
    more info
     

    General protein information

    Preferred Names
    kin of IRRE-like protein 3
    Names
    kin of IRRE like 3
    kin of irregular chiasm-like protein 3
    nephrin-like 2
    nephrin-like protein 2

    NCBI Reference Sequences (RefSeq)

    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_012971.1 RefSeqGene

      Range
      5001..582371
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001161707.1NP_001155179.1  kin of IRRE-like protein 3 isoform 2 precursor

      See identical proteins and their annotated locations for NP_001155179.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) includes an alternate segment at the 3' end compared to variant 1. This results in a frame-shift, and a shorter isoform (2) with a distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AY358743, BC065255
      Consensus CDS
      CCDS55796.1
      UniProtKB/Swiss-Prot
      Q8IZU9
      Related
      ENSP00000435094.2, OTTHUMP00000231132, ENST00000525704.2, OTTHUMT00000386483
      Conserved Domains (7) summary
      cd05759
      Location:165246
      Ig2_KIRREL3-like; Second immunoglobulin (Ig)-like domain of Kirrel (kin of irregular chiasm-like) 3 (also known as Neph2)
      cd05898
      Location:418515
      Ig5_KIRREL3; Fifth immunoglobulin (Ig)-like domain of Kirrel (kin of irregular chiasm-like) 3 protein (also known as Neph2)
      smart00408
      Location:349400
      IGc2; Immunoglobulin C-2 Type
      smart00410
      Location:426515
      IG_like; Immunoglobulin like
      pfam07679
      Location:335416
      I-set; Immunoglobulin I-set domain
      pfam13895
      Location:254331
      Ig_2; Immunoglobulin domain
      cl11960
      Location:52143
      Ig; Immunoglobulin domain
    2. NM_001301097.1NP_001288026.1  kin of IRRE-like protein 3 isoform 3 precursor

      See identical proteins and their annotated locations for NP_001288026.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (3) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AP000806, BC042432, BC065255, BM671831
      Consensus CDS
      CCDS73413.1
      UniProtKB/TrEMBL
      E9PRX9
      Related
      ENSP00000434081.2, OTTHUMP00000231131, ENST00000529097.6, OTTHUMT00000386480
      Conserved Domains (7) summary
      cd05759
      Location:165246
      Ig2_KIRREL3-like; Second immunoglobulin (Ig)-like domain of Kirrel (kin of irregular chiasm-like) 3 (also known as Neph2)
      cd05898
      Location:418515
      Ig5_KIRREL3; Fifth immunoglobulin (Ig)-like domain of Kirrel (kin of irregular chiasm-like) 3 protein (also known as Neph2)
      smart00408
      Location:349400
      IGc2; Immunoglobulin C-2 Type
      smart00410
      Location:426515
      IG_like; Immunoglobulin like
      pfam07679
      Location:335416
      I-set; Immunoglobulin I-set domain
      pfam13895
      Location:254331
      Ig_2; Immunoglobulin domain
      cl11960
      Location:52143
      Ig; Immunoglobulin domain
    3. NM_032531.3NP_115920.1  kin of IRRE-like protein 3 isoform 1 precursor

      See identical proteins and their annotated locations for NP_115920.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AB058770, AY358760, BC065255, BC101801, BM671831, W75978
      Consensus CDS
      CCDS53723.1
      UniProtKB/Swiss-Prot
      Q8IZU9
      Related
      ENSP00000435466.2, OTTHUMP00000231130, ENST00000525144.6, OTTHUMT00000386479
      Conserved Domains (7) summary
      cd05759
      Location:165246
      Ig2_KIRREL3-like; Second immunoglobulin (Ig)-like domain of Kirrel (kin of irregular chiasm-like) 3 (also known as Neph2)
      cd05898
      Location:418515
      Ig5_KIRREL3; Fifth immunoglobulin (Ig)-like domain of Kirrel (kin of irregular chiasm-like) 3 protein (also known as Neph2)
      smart00408
      Location:349400
      IGc2; Immunoglobulin C-2 Type
      smart00410
      Location:426515
      IG_like; Immunoglobulin like
      pfam07679
      Location:335416
      I-set; Immunoglobulin I-set domain
      pfam13895
      Location:254331
      Ig_2; Immunoglobulin domain
      cl11960
      Location:52143
      Ig; Immunoglobulin domain

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

    Reference GRCh38.p12 Primary Assembly

    Genomic

    1. NC_000011.10 Reference GRCh38.p12 Primary Assembly

      Range
      126423493..127003460 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011543033.1XP_011541335.1  kin of IRRE-like protein 3 isoform X7

      See identical proteins and their annotated locations for XP_011541335.1

      UniProtKB/TrEMBL
      E9PRX9
      Conserved Domains (7) summary
      cd05759
      Location:165246
      Ig2_KIRREL3-like; Second immunoglobulin (Ig)-like domain of Kirrel (kin of irregular chiasm-like) 3 (also known as Neph2)
      cd05898
      Location:418515
      Ig5_KIRREL3; Fifth immunoglobulin (Ig)-like domain of Kirrel (kin of irregular chiasm-like) 3 protein (also known as Neph2)
      smart00408
      Location:349400
      IGc2; Immunoglobulin C-2 Type
      smart00410
      Location:426515
      IG_like; Immunoglobulin like
      pfam07679
      Location:335416
      I-set; Immunoglobulin I-set domain
      pfam13895
      Location:254331
      Ig_2; Immunoglobulin domain
      cl11960
      Location:52143
      Ig; Immunoglobulin domain
    2. XM_017018419.1XP_016873908.1  kin of IRRE-like protein 3 isoform X3

    3. XM_011543027.2XP_011541329.1  kin of IRRE-like protein 3 isoform X2

      See identical proteins and their annotated locations for XP_011541329.1

      Conserved Domains (7) summary
      cd05759
      Location:165246
      Ig2_KIRREL3-like; Second immunoglobulin (Ig)-like domain of Kirrel (kin of irregular chiasm-like) 3 (also known as Neph2)
      cd05898
      Location:418515
      Ig5_KIRREL3; Fifth immunoglobulin (Ig)-like domain of Kirrel (kin of irregular chiasm-like) 3 protein (also known as Neph2)
      smart00408
      Location:349400
      IGc2; Immunoglobulin C-2 Type
      smart00410
      Location:426515
      IG_like; Immunoglobulin like
      pfam07679
      Location:335416
      I-set; Immunoglobulin I-set domain
      pfam13895
      Location:254331
      Ig_2; Immunoglobulin domain
      cl11960
      Location:52143
      Ig; Immunoglobulin domain
    4. XM_011543031.2XP_011541333.1  kin of IRRE-like protein 3 isoform X5

      See identical proteins and their annotated locations for XP_011541333.1

      UniProtKB/Swiss-Prot
      Q8IZU9
      Conserved Domains (7) summary
      cd05759
      Location:165246
      Ig2_KIRREL3-like; Second immunoglobulin (Ig)-like domain of Kirrel (kin of irregular chiasm-like) 3 (also known as Neph2)
      cd05898
      Location:418515
      Ig5_KIRREL3; Fifth immunoglobulin (Ig)-like domain of Kirrel (kin of irregular chiasm-like) 3 protein (also known as Neph2)
      smart00408
      Location:349400
      IGc2; Immunoglobulin C-2 Type
      smart00410
      Location:426515
      IG_like; Immunoglobulin like
      pfam07679
      Location:335416
      I-set; Immunoglobulin I-set domain
      pfam13895
      Location:254331
      Ig_2; Immunoglobulin domain
      cl11960
      Location:52143
      Ig; Immunoglobulin domain
    5. XM_017018420.1XP_016873909.1  kin of IRRE-like protein 3 isoform X5

      UniProtKB/Swiss-Prot
      Q8IZU9
      Conserved Domains (7) summary
      cd05759
      Location:165246
      Ig2_KIRREL3-like; Second immunoglobulin (Ig)-like domain of Kirrel (kin of irregular chiasm-like) 3 (also known as Neph2)
      cd05898
      Location:418515
      Ig5_KIRREL3; Fifth immunoglobulin (Ig)-like domain of Kirrel (kin of irregular chiasm-like) 3 protein (also known as Neph2)
      smart00408
      Location:349400
      IGc2; Immunoglobulin C-2 Type
      smart00410
      Location:426515
      IG_like; Immunoglobulin like
      pfam07679
      Location:335416
      I-set; Immunoglobulin I-set domain
      pfam13895
      Location:254331
      Ig_2; Immunoglobulin domain
      cl11960
      Location:52143
      Ig; Immunoglobulin domain
    6. XM_011543028.2XP_011541330.1  kin of IRRE-like protein 3 isoform X2

      See identical proteins and their annotated locations for XP_011541330.1

      Conserved Domains (7) summary
      cd05759
      Location:165246
      Ig2_KIRREL3-like; Second immunoglobulin (Ig)-like domain of Kirrel (kin of irregular chiasm-like) 3 (also known as Neph2)
      cd05898
      Location:418515
      Ig5_KIRREL3; Fifth immunoglobulin (Ig)-like domain of Kirrel (kin of irregular chiasm-like) 3 protein (also known as Neph2)
      smart00408
      Location:349400
      IGc2; Immunoglobulin C-2 Type
      smart00410
      Location:426515
      IG_like; Immunoglobulin like
      pfam07679
      Location:335416
      I-set; Immunoglobulin I-set domain
      pfam13895
      Location:254331
      Ig_2; Immunoglobulin domain
      cl11960
      Location:52143
      Ig; Immunoglobulin domain
    7. XM_011543026.2XP_011541328.1  kin of IRRE-like protein 3 isoform X1

      Conserved Domains (7) summary
      cd05759
      Location:171252
      Ig2_KIRREL3-like; Second immunoglobulin (Ig)-like domain of Kirrel (kin of irregular chiasm-like) 3 (also known as Neph2)
      cd05898
      Location:424521
      Ig5_KIRREL3; Fifth immunoglobulin (Ig)-like domain of Kirrel (kin of irregular chiasm-like) 3 protein (also known as Neph2)
      smart00408
      Location:355406
      IGc2; Immunoglobulin C-2 Type
      smart00410
      Location:432521
      IG_like; Immunoglobulin like
      pfam07679
      Location:341422
      I-set; Immunoglobulin I-set domain
      pfam13895
      Location:260337
      Ig_2; Immunoglobulin domain
      cl11960
      Location:58149
      Ig; Immunoglobulin domain
    8. XM_011543032.3XP_011541334.1  kin of IRRE-like protein 3 isoform X6

      Conserved Domains (7) summary
      cd05759
      Location:171252
      Ig2_KIRREL3-like; Second immunoglobulin (Ig)-like domain of Kirrel (kin of irregular chiasm-like) 3 (also known as Neph2)
      cd05898
      Location:424521
      Ig5_KIRREL3; Fifth immunoglobulin (Ig)-like domain of Kirrel (kin of irregular chiasm-like) 3 protein (also known as Neph2)
      smart00408
      Location:355406
      IGc2; Immunoglobulin C-2 Type
      smart00410
      Location:432521
      IG_like; Immunoglobulin like
      pfam07679
      Location:341422
      I-set; Immunoglobulin I-set domain
      pfam13895
      Location:260337
      Ig_2; Immunoglobulin domain
      cl11960
      Location:58149
      Ig; Immunoglobulin domain
    9. XM_011543030.3XP_011541332.1  kin of IRRE-like protein 3 isoform X4

      Conserved Domains (7) summary
      cd05759
      Location:171252
      Ig2_KIRREL3-like; Second immunoglobulin (Ig)-like domain of Kirrel (kin of irregular chiasm-like) 3 (also known as Neph2)
      cd05898
      Location:424521
      Ig5_KIRREL3; Fifth immunoglobulin (Ig)-like domain of Kirrel (kin of irregular chiasm-like) 3 protein (also known as Neph2)
      smart00408
      Location:355406
      IGc2; Immunoglobulin C-2 Type
      smart00410
      Location:432521
      IG_like; Immunoglobulin like
      pfam07679
      Location:341422
      I-set; Immunoglobulin I-set domain
      pfam13895
      Location:260337
      Ig_2; Immunoglobulin domain
      cl11960
      Location:58149
      Ig; Immunoglobulin domain
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