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    SNX3 sorting nexin 3 [ Homo sapiens (human) ]

    Gene ID: 8724, updated on 3-Nov-2024

    Summary

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    Official Symbol
    SNX3provided by HGNC
    Official Full Name
    sorting nexin 3provided by HGNC
    Primary source
    HGNC:HGNC:11174
    See related
    Ensembl:ENSG00000112335 MIM:605930; AllianceGenome:HGNC:11174
    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
    SDP3; Grd19; MCOPS8
    Summary
    This gene encodes a member of the sorting nexin family. Members of this family contain a phox (PX) domain, which is a phosphoinositide binding domain, and are involved in intracellular trafficking. This protein does not contain a coiled coil region, like most family members. This protein interacts with phosphatidylinositol-3-phosphate, and is involved in protein trafficking. A pseudogene of this gene is present on the sex chromosomes. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jul 2014]
    Expression
    Ubiquitous expression in fat (RPKM 95.7), adrenal (RPKM 90.6) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SNX3 in Genome Data Viewer
    Location:
    6q21
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (108211222..108261040, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (109388338..109438159, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (108532426..108582244, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr6:108488071-108488972 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:108489873-108490774 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:108490775-108491674 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:108497591-108498326 Neighboring gene Sharpr-MPRA regulatory region 5034 Neighboring gene uncharacterized LOC124901369 Neighboring gene nuclear receptor subfamily 2 group E member 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24910 Neighboring gene MPRA-validated peak6010 silencer Neighboring gene MPRA-validated peak6011 silencer Neighboring gene small nucleolar RNA U13 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17448 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17449 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:108582429-108583264 Neighboring gene RNA, 5S ribosomal pseudogene 212 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:108603498-108603672 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17450 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24911 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24912 Neighboring gene RNA, U6 small nuclear 1144, pseudogene Neighboring gene AFG1 like ATPase Neighboring gene ribosomal protein L36a pseudogene 24

    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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    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Sorting nexin 3 induces heart failure via promoting retromer-dependent nuclear trafficking of STAT3.
      Title: Sorting nexin 3 induces heart failure via promoting retromer-dependent nuclear trafficking of STAT3.
    2. LINC01614 promotes osteosarcoma progression via miR-520a-3p/SNX3 axis.
      Title: LINC01614 promotes osteosarcoma progression via miR-520a-3p/SNX3 axis.
    3. sorting nexin SNX3 is transported with Rab5a vesicles and that its PX domain enables vesicle-phagosome contact by binding to PI(3)P in the phagosomal coat. Moreover, the C-terminal region of SNX3 recruits galectin-9, a lectin implicated in protein and membrane recycling, which we identify as a further regulator of phagosome compaction.
      Title: SNX3 drives maturation of Borrelia phagosomes by forming a hub for PI(3)P, Rab5a, and galectin-9.
    4. SNX3 regulates amyloid beta production by influencing the internalization of amyloid precursor protein in HEK293T cells and may have a role in the pathogenesis of Alzheimer's disease.
      Title: Overexpression of SNX3 Decreases Amyloid-β Peptide Production by Reducing Internalization of Amyloid Precursor Protein.
    5. an evolutionary conserved MON2:DOPEY2:ATP9A complex is required for SNX3 retromer mediation of Wntless sorting and Wnt secretion
      Title: SNX3-retromer requires an evolutionary conserved MON2:DOPEY2:ATP9A complex to mediate Wntless sorting and Wnt secretion.
    6. SNX3-retromer complex regulates the surface expression and function of PC1 and PC2
      Title: The Sorting Nexin 3 Retromer Pathway Regulates the Cell Surface Localization and Activity of a Wnt-Activated Polycystin Channel Complex.
    7. X-ray crystallographic analysis of a 4-component complex comprising the VPS26 & VPS35 subunits of retromer, sorting nexin SNX3, & recycling signal from the divalent cation transporter DMT1-II; analysis identifies a binding site for canonical recycling signals at the interface between VPS26 & SNX3; shows cooperative interactions among the VPS subunits, SNX3 & cargo that couple signal-recognition to membrane recruitment.
      Title: Structural Mechanism for Cargo Recognition by the Retromer Complex.
    8. Data show that over-expression of sorting nexin 3 (hSNX3) alters the morphology of colon cancer SW620 cells, but hardly affects cell migration.
      Title: [The morphological changes of SW620 cells induced by over-expression of human sorting nexin 3].
    9. SNX3 negatively regulates phagocytosis in DC possibly by modulating recruitment of essential PI3P lipid-binding proteins of the phagocytic pathways, such as EEA1, to phagosomal membranes.
      Title: SNX3 recruits to phagosomes and negatively regulates phagocytosis in dendritic cells.
    10. This study found that four significant SNX3 SNPs in the discovery sample were replicated in a community-based sample of Israeli-Arabs
      Title: Identification of Alzheimer disease-associated variants in genes that regulate retromer function.
    Submit: New GeneRIF Correction See all GeneRIFs (16)

    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

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC17570

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables phosphatidylinositol-3,5-bisphosphate binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables phosphatidylinositol-3-phosphate binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables phosphatidylinositol-3-phosphate binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables phosphatidylinositol-4-phosphate binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables phosphatidylinositol-5-phosphate binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein phosphatase binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables retromer complex binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in endocytic recycling IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in intralumenal vesicle formation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in late endosome to Golgi transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in membrane invagination IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of early endosome to late endosome transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of phagocytosis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of protein catabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of protein transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of viral entry into host cell IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of neuron projection development ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in protein to membrane docking IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of Wnt signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in response to bacterium IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in clathrin-coated vesicle IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in early endosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in early endosome membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in early endosome membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in early phagosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in endosome membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in endosome membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in extracellular exosome HDA PubMed 
    part_of retromer complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of retromer complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    sorting nexin-3
    Names
    sorting nexin 3A

    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_023278.1 RefSeqGene

      Range
      5221..55039
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001300928.2 → NP_001287857.1  sorting nexin-3 isoform c

      See identical proteins and their annotated locations for NP_001287857.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an exon in the 3' coding region, compared to variant 1, which results in a frameshift and a protein (isoform c) with a shorter and distinct C-terminus, compared to isoform a.
      Source sequence(s)
      AI921483, BQ432490, CA442762, CN422502, HY156437
      Conserved Domains (1) summary
      cl02563
      Location:28 → 86
      PX_domain; The Phox Homology domain, a phosphoinositide binding module

    2. NM_001300929.2 → NP_001287858.1  sorting nexin-3 isoform d

      See identical proteins and their annotated locations for NP_001287858.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks an in-frame portion of the first coding exon, compared to variant 1. It encodes isoform d, which is shorter than isoform a.
      Source sequence(s)
      AI921483, BQ432490, CA442762, CN422502, HY023148
      Consensus CDS
      CCDS75501.1
      UniProtKB/Swiss-Prot
      O60493
      Related
      ENSP00000296991.7, ENST00000349379.5
      Conserved Domains (1) summary
      cl02563
      Location:12 → 128
      PX_domain; The Phox Homology domain, a phosphoinositide binding module

    3. NM_003795.6 → NP_003786.1  sorting nexin-3 isoform a

      See identical proteins and their annotated locations for NP_003786.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
      Source sequence(s)
      AF034546, BQ432490, CA442762, HY023148
      Consensus CDS
      CCDS5064.1
      UniProtKB/Swiss-Prot
      A8K0B1, E1P5E4, E1P5E5, O60493, O60718, Q4TT29, Q4TT31, Q5JXJ7, Q5JXJ8, Q96AP9, Q9C0J5, Q9NU45
      Related
      ENSP00000230085.8, ENST00000230085.13
      Conserved Domains (1) summary
      cd07293
      Location:28 → 150
      PX_SNX3; The phosphoinositide binding Phox Homology domain of Sorting Nexin 3

    4. NM_152827.4 → NP_690040.1  sorting nexin-3 isoform b

      See identical proteins and their annotated locations for NP_690040.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an in-frame coding exon, compared to variant 1. It encodes isoform b, also known as SNX3A, which is shorter than isoform a.
      Source sequence(s)
      AB047360, BQ432490, CA442762, HY023148
      Consensus CDS
      CCDS5065.1
      UniProtKB/Swiss-Prot
      O60493
      Related
      ENSP00000401779.2, ENST00000426155.6
      Conserved Domains (1) summary
      cl02563
      Location:28 → 118
      PX_domain; The Phox Homology domain, a phosphoinositide binding module

    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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      108211222..108261040 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      109388338..109438159 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_152828.2: Suppressed sequence

      Description
      NM_152828.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein, and because the transcript is a nonsense-mediated mRNA decay (NMD) candidate.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O60493.3 GenPept UniProtKB/Swiss-Prot:O60493

    Gene LinkOut

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

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