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

Gene ID: 84623, updated on 11-Jun-2021

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
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
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Genomic context

See KIRREL3 in Genome Data Viewer
Location:
11q24.2
Exon count:
19
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 11 NC_000011.10 (126423358..127003460, complement)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (126293253..126870766, complement)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene ST3 beta-galactoside alpha-2,3-sialyltransferase 4 Neighboring gene Sharpr-MPRA regulatory region 5906 Neighboring gene uncharacterized LOC101929427 Neighboring gene Sharpr-MPRA regulatory region 13423 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 Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
A genome-wide association study identifies protein quantitative trait loci (pQTLs).
GeneReviews: Not available
Conduct disorder and ADHD: evaluation of conduct problems as a categorical and quantitative trait in the international multicentre ADHD genetics study.
GeneReviews: Not available
Genetic variants associated with breast size also influence breast cancer risk.
GeneReviews: Not available
Genome wide association study of age at menarche in the Japanese population.
GeneReviews: Not available
Genomewide pharmacogenomic study of metabolic side effects to antipsychotic drugs.
GeneReviews: Not available
Web-based, participant-driven studies yield novel genetic associations for common traits.
GeneReviews: Not available

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
enables cell adhesion molecule binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
involved_in cell-cell adhesion IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in glomerulus morphogenesis IEA
Inferred from Electronic Annotation
more info
 
involved_in hemopoiesis ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in hippocampus development ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in homophilic cell adhesion via plasma membrane adhesion molecules ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in inter-male aggressive behavior IEA
Inferred from Electronic Annotation
more info
 
involved_in neuron migration IEA
Inferred from Electronic Annotation
more info
 
involved_in neuron projection morphogenesis IEA
Inferred from Electronic Annotation
more info
 
involved_in principal sensory nucleus of trigeminal nerve development IEA
Inferred from Electronic Annotation
more info
 
involved_in synapse assembly IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in synapse assembly ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
located_in axon ISS
Inferred from Sequence or Structural Similarity
more info
 
is_active_in cell-cell junction IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in dendrite ISS
Inferred from Sequence or Structural Similarity
more info
 
located_in dendritic shaft IEA
Inferred from Electronic Annotation
more info
 
located_in extracellular region ISS
Inferred from Sequence or Structural Similarity
more info
 
located_in integral component of membrane ISS
Inferred from Sequence or Structural Similarity
more info
 
is_active_in integral component of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in plasma membrane TAS
Traceable Author Statement
more info
 
located_in synaptic vesicle IDA
Inferred from Direct Assay
more info
PubMed 

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)

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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_012971.1 RefSeqGene

    Range
    5101..582514
    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, ENST00000525704.2
    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, ENST00000529097.6
    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_032531.4NP_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, AP000806, AY358760, BC065255, BC101801, BM671831, W75978
    Consensus CDS
    CCDS53723.1
    UniProtKB/Swiss-Prot
    Q8IZU9
    Related
    ENSP00000435466.2, ENST00000525144.7
    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 Updated Annotation Release 109.20210514

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p13 Primary Assembly

    Range
    126423358..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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