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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
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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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Related articles in PubMed

  1. Overexpression of SNX3 Decreases Amyloid-β Peptide Production by Reducing Internalization of Amyloid Precursor Protein. Xu S, et al. Neurodegener Dis, 2018. PMID 29414832, Free PMC Article
  2. Sorting nexin 3 (SNX3) is disrupted in a patient with a translocation t(6;13)(q21;q12) and microcephaly, microphthalmia, ectrodactyly, prognathism (MMEP) phenotype. Vervoort VS, et al. J Med Genet, 2002 Dec. PMID 12471201, Free PMC Article
  3. [The morphological changes of SW620 cells induced by over-expression of human sorting nexin 3]. Yang W, et al. Xi Bao Yu Fen Zi Mian Yi Xue Za Zhi, 2015 Aug. PMID 26271979
  4. Absence of mutations in NR2E1 and SNX3 in five patients with MMEP (microcephaly, microphthalmia, ectrodactyly, and prognathism) and related phenotypes. Kumar RA, et al. BMC Med Genet, 2007 Jul 26. PMID 17655765, Free PMC Article
  5. SNX3-dependent regulation of epidermal growth factor receptor (EGFR) trafficking and degradation by aspirin in epidermoid carcinoma (A-431) cells. Chiow KH, et al. Cell Mol Life Sci, 2012 May. PMID 22159558, Free PMC Article

See all (85) citations in PubMed

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)

Genotypes

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

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