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    ASTN2 astrotactin 2 [ Homo sapiens (human) ]

    Gene ID: 23245, updated on 2-Nov-2024

    Summary

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    Official Symbol
    ASTN2provided by HGNC
    Official Full Name
    astrotactin 2provided by HGNC
    Primary source
    HGNC:HGNC:17021
    See related
    Ensembl:ENSG00000148219 MIM:612856; AllianceGenome:HGNC:17021
    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
    bA67K19.1
    Summary
    This gene encodes a protein that is expressed in the brain and may function in neuronal migration, based on functional studies of the related astrotactin 1 gene in human and mouse. A deletion at this locus has been associated with schizophrenia. Multiple transcript variants encoding different proteins have been found for this locus. [provided by RefSeq, May 2010]
    Expression
    Biased expression in prostate (RPKM 6.8), brain (RPKM 6.4) and 13 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ASTN2 in Genome Data Viewer
    Location:
    9q33.1
    Exon count:
    25
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (116423112..117415057, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (128616101..129608884, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (119185391..120177335, complement)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:119048252-119048828 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:119048829-119049403 Neighboring gene pappalysin 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:119093474-119094066 Neighboring gene PAPPA antisense RNA 2 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:119117289-119117861 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28883 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20220 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:119157715-119158214 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:119185010-119185266 Neighboring gene PAPPA antisense RNA 1 Neighboring gene GATA motif-containing MPRA enhancer 254 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr9:119233696-119234286 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr9:119233104-119233695 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:119243946-119244892 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_106426 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr9:119301784-119302983 Neighboring gene Sharpr-MPRA regulatory region 10185 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_106457 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_106460 Neighboring gene ASTN2 antisense RNA 1 Neighboring gene uncharacterized LOC107987014 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:119352121-119352680 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:119352681-119353238 Neighboring gene uncharacterized LOC105376240 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28884 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20221 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28885 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:119562284-119563028 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:119564021-119564522 Neighboring gene tripartite motif containing 32 Neighboring gene uncharacterized LOC105376239 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:119602872-119603616 Neighboring gene uncharacterized LOC105376238 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr9:119690983-119691925 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:119833416-119834008 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:119834009-119834601 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr9:119857782-119858981 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:119875735-119875911 Neighboring gene uncharacterized LOC105376237 Neighboring gene RN7SK pseudogene 128 Neighboring gene small nucleolar RNA, H/ACA box 70C Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:120031095-120031743 Neighboring gene ribosomal protein L10 pseudogene 3 Neighboring gene RN7SK pseudogene 125 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:120117495-120117996 Neighboring gene uncharacterized LOC105376242 Neighboring gene uncharacterized LOC124902330 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28886 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:120311686-120312295 Neighboring gene uncharacterized LOC101928797

    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 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. Genetic Variation in the ASTN2 Locus in Cardiovascular, Metabolic and Psychiatric Traits: Evidence for Pleiotropy Rather Than Shared Biology. Burt O, et al. Genes (Basel), 2021 Jul 31. PMID 34440368, Free PMC Article
    2. Rare copy number variation discovery and cross-disorder comparisons identify risk genes for ADHD. Lionel AC, et al. Sci Transl Med, 2011 Aug 10. PMID 21832240
    3. Polymorphisms within ASTN2 gene are associated with age at onset of Alzheimer's disease. Wang KS, et al. J Neural Transm (Vienna), 2015 May. PMID 25410587
    4. The role of ASTN2 variants in childhood and adult ADHD, comorbid disorders and associated personality traits. Freitag CM, et al. J Neural Transm (Vienna), 2016 Aug. PMID 27138430
    5. Structure of astrotactin-2: a conserved vertebrate-specific and perforin-like membrane protein involved in neuronal development. Ni T, et al. Open Biol, 2016 May. PMID 27249642, Free PMC Article

    See all (44) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Genetic Variation in the ASTN2 Locus in Cardiovascular, Metabolic and Psychiatric Traits: Evidence for Pleiotropy Rather Than Shared Biology.
      Title: Genetic Variation in the ASTN2 Locus in Cardiovascular, Metabolic and Psychiatric Traits: Evidence for Pleiotropy Rather Than Shared Biology.
    2. Rare copy number variants in ASTN2 gene in patients with neurodevelopmental disorders.
      Title: Rare copy number variants in ASTN2 gene in patients with neurodevelopmental disorders.
    3. Effects of rs958804 and rs7858836 single-nucleotide polymorphisms of the ASTN2 gene on pain-related phenotypes in patients who underwent laparoscopic colectomy and mandibular sagittal split ramus osteotomy.
      Title: Effects of rs958804 and rs7858836 single-nucleotide polymorphisms of the ASTN2 gene on pain-related phenotypes in patients who underwent laparoscopic colectomy and mandibular sagittal split ramus osteotomy.
    4. Chimeric RNA ASTN2-PAPPAas aggravates tumor progression and metastasis in human esophageal cancer.
      Title: Chimeric RNA ASTN2-PAPPA(as) aggravates tumor progression and metastasis in human esophageal cancer.
    5. ASTN2 localizes primarily to endocytic and autophagocytic vesicles in the cell soma and in subsets of dendritic spines
      Title: ASTN2 modulates synaptic strength by trafficking and degradation of surface proteins.
    6. Our study suggests that the MEF2D, PRDM16 and ASTN2 genes from GWAS are associated with migraine susceptibility, especially migraine without aura , among Chinese patients. It appears that there is no association with serotonin receptor related genes.
      Title: Multilocus analysis reveals three candidate genes for Chinese migraine susceptibility.
    7. The findings of this study do not support a major role of ASTN2 variants in ADHD or its comorbid disorders respective aADHD associated personality traits.
      Title: The role of ASTN2 variants in childhood and adult ADHD, comorbid disorders and associated personality traits.
    8. Results present the structure of ASTN-2 consisting of a combination of polypeptide folds: a perforin-like domain, a minimal epidermal growth factor-like module, a unique form of fibronectin type III domain and an annexin-like domain. Structural and biophysical data show that ASTN-2 binds inositol triphosphates, suggesting a mechanism for membrane recognition or secondary messenger regulation of its activity.
      Title: Structure of astrotactin-2: a conserved vertebrate-specific and perforin-like membrane protein involved in neuronal development.
    9. The expression of coding and non-coding genes with SAFB1 cross-link sites was altered by SAFB1 knockdown. The isoform-specific expression of neural cell adhesion molecule (NCAM1) and ASTN2 was influenced by SAFB1.
      Title: iCLIP identifies novel roles for SAFB1 in regulating RNA processing and neuronal function.
    10. Study found a significant association of ASTN2 genetic variants with age at onset in Alzheimer's disease in two independent samples together with in silico analysis that demonstrated potential role of ASTN2 in the pathogenesis of the disease
      Title: Polymorphisms within ASTN2 gene are associated with age at onset of Alzheimer's disease.
    Submit: New GeneRIF Correction See all GeneRIFs (18)

    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

    Copy number response

    Description
    Copy number response
    Haploinsufficency

    Little evidence for dosage pathogenicity (Last evaluated 2021-03-09)

    ClinGen Genome Curation PagePubMed
    Triplosensitivity

    No evidence available (Last evaluated 2021-03-09)

    ClinGen Genome Curation Page

    EBI GWAS Catalog

    Description
    A genome-wide association study of host genetic determinants of the antibody response to Anthrax Vaccine Adsorbed.
    EBI GWAS Catalog
    A genome-wide meta-analysis identifies novel loci associated with schizophrenia and bipolar disorder.
    EBI GWAS Catalog
    Common variants at 12q14 and 12q24 are associated with hippocampal volume.
    EBI GWAS Catalog
    Genome-wide association analysis identifies susceptibility loci for migraine without aura.
    EBI GWAS Catalog
    Genome-wide association study of smoking behaviours in patients with COPD.
    EBI GWAS Catalog
    Genome-wide joint meta-analysis of SNP and SNP-by-smoking interaction identifies novel loci for pulmonary function.
    EBI GWAS Catalog
    Genome-wide meta-analysis identifies new susceptibility loci for migraine.
    EBI GWAS Catalog
    Genomewide pharmacogenomic study of metabolic side effects to antipsychotic drugs.
    EBI GWAS Catalog
    Molecular genetics of adult ADHD: converging evidence from genome-wide association and extended pedigree linkage studies.
    EBI GWAS Catalog
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    EBI GWAS Catalog
    The genetic architecture of economic and political preferences.
    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

    • KIAA0634, bA264C15.1

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables calcium ion binding IDA
    Inferred from Direct Assay
    more info
    		  
    enables inositol 1,3,4,5 tetrakisphosphate binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables inositol 1,3,4,5 tetrakisphosphate binding IDA
    Inferred from Direct Assay
    more info
    		  
    Process Evidence Code Pubs
    involved_in establishment of body hair planar orientation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of protein localization to cell surface IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in neuron cell-cell adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in neuron migration IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein localization to cell surface IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cell cortex IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cell pole IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in clathrin-coated vesicle IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in early endosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in endosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in late endosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in perikaryon IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    astrotactin-2

    NCBI Reference Sequences (RefSeq)

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    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_021409.2 RefSeqGene

      Range
      5001..996946
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001184734.1 → NP_001171663.1  astrotactin-2 isoform e

      See identical proteins and their annotated locations for NP_001171663.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. This variant also lacks a segment in the 3' coding region compared to variant 1. The encoded isoform (e) has distinct N- and C-termini and is shorter than isoform a.
      Source sequence(s)
      AI341147, BC143292, DA015423
      UniProtKB/TrEMBL
      B7ZKP3, B7ZKP4
      Conserved Domains (2) summary
      cd00063
      Location:131 → 240
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      cl02616
      Location:1 → 87
      MACPF; MAC/Perforin domain

    2. NM_001184735.1 → NP_001171664.1  astrotactin-2 isoform f

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) has multiple differences compared to variant 1. These differences result in a distinct 5' UTR and lead to translation initiation at an alternate start codon, compared to variant 1. The encoded isoform (f) has distinct N- and C-termini and is shorter than isoform a.
      Source sequence(s)
      AK024064, AL133284, BC010680, DA015423
      Consensus CDS
      CCDS55334.1
      UniProtKB/TrEMBL
      X6R5P2
      Related
      ENSP00000351460.4, ENST00000358637.4
      Conserved Domains (1) summary
      cl02616
      Location:1 → 87
      MACPF; MAC/Perforin domain

    3. NM_001365068.1 → NP_001351997.1  astrotactin-2 isoform g precursor

      Status: REVIEWED

      Source sequence(s)
      AL133282, AL133284, AL137024, AL157829, AL354981, AL355608, AL358792, AL392085
      Consensus CDS
      CCDS6816.1
      UniProtKB/Swiss-Prot
      A2A2T7, A2A2T9, O75129, Q52LQ2, Q5JVX8, Q5JVX9, Q5JVY1, Q5VXG8, Q5VZX6, Q8N6P8, Q8WV47, Q96FL4, Q9UHW6
      UniProtKB/TrEMBL
      A0A0A0MRH9
      Related
      ENSP00000314038.4, ENST00000313400.9
      Conserved Domains (2) summary
      smart00457
      Location:852 → 1035
      MACPF; membrane-attack complex / perforin
      pfam14670
      Location:703 → 750
      FXa_inhibition; Coagulation Factor Xa inhibitory site

    4. NM_001365069.1 → NP_001351998.1  astrotactin-2 isoform h precursor

      Status: REVIEWED

      Source sequence(s)
      AL133282, AL133284, AL137024, AL157829, AL354981, AL355608, AL358792, AL392085
      UniProtKB/TrEMBL
      A0A0A0MRH9
      Conserved Domains (2) summary
      smart00457
      Location:848 → 1031
      MACPF; membrane-attack complex / perforin
      pfam14670
      Location:699 → 746
      FXa_inhibition; Coagulation Factor Xa inhibitory site

    5. NM_014010.5 → NP_054729.3  astrotactin-2 isoform a precursor

      See identical proteins and their annotated locations for NP_054729.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
      Source sequence(s)
      AL133282, AL133284, AL137024, AL157829, AL354981, AL355608, AL358792, AL392085
      Consensus CDS
      CCDS6815.1
      UniProtKB/TrEMBL
      A0A0A0MRH9
      Related
      ENSP00000354504.2, ENST00000361209.6
      Conserved Domains (2) summary
      smart00457
      Location:801 → 984
      MACPF; membrane-attack complex / perforin
      pfam14670
      Location:652 → 699
      FXa_inhibition; Coagulation Factor Xa inhibitory site

    6. NM_198186.3 → NP_937829.3  astrotactin-2 isoform b

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (b) has a distinct N-terminus and is shorter than isoform a.
      Source sequence(s)
      AI341147, BC029272, BX649176
      Consensus CDS
      CCDS48009.2
      UniProtKB/TrEMBL
      B7ZKP3
      Related
      ENSP00000288520.5, ENST00000288520.9
      Conserved Domains (2) summary
      cd00063
      Location:169 → 289
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      cl02616
      Location:42 → 136
      MACPF; MAC/Perforin domain

    7. NM_198187.3 → NP_937830.3  astrotactin-2 isoform c

      See identical proteins and their annotated locations for NP_937830.3

      Status: REVIEWED

      Source sequence(s)
      AI341147, BC143293, DA015423
      UniProtKB/TrEMBL
      B3KN99, B7ZKP5
      Conserved Domains (2) summary
      cd00063
      Location:131 → 240
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      cl02616
      Location:1 → 87
      MACPF; MAC/Perforin domain

    8. NM_198188.2 → NP_937831.1  astrotactin-2 isoform d

      See identical proteins and their annotated locations for NP_937831.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. This variant also lacks a segment in the 3' coding region compared to variant 1. The encoded isoform (d) has distinct N- and C-termini and is shorter than isoform a.
      Source sequence(s)
      AI341147, AK024064, BC093835, DA015423
      Consensus CDS
      CCDS6814.1
      UniProtKB/TrEMBL
      B3KN99
      Related
      ENSP00000339925.4, ENST00000341734.8
      Conserved Domains (2) summary
      cd00063
      Location:131 → 240
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      cl02616
      Location:1 → 87
      MACPF; MAC/Perforin domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      116423112..117415057 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      128616101..129608884 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O75129.2 GenPept UniProtKB/Swiss-Prot:O75129

    Gene LinkOut

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

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