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    SNX1 sorting nexin 1 [ Homo sapiens (human) ]

    Gene ID: 6642, updated on 17-Jun-2024

    Summary

    Official Symbol
    SNX1provided by HGNC
    Official Full Name
    sorting nexin 1provided by HGNC
    Primary source
    HGNC:HGNC:11172
    See related
    Ensembl:ENSG00000028528 MIM:601272; AllianceGenome:HGNC:11172
    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
    VPS5; HsT17379
    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 endosomal protein regulates the cell-surface expression of epidermal growth factor receptor. This protein also has a role in sorting protease-activated receptor-1 from early endosomes to lysosomes. This protein may form oligomeric complexes with family members. This gene results in three transcript variants encoding distinct isoforms. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in thyroid (RPKM 29.5), fat (RPKM 17.2) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SNX1 in Genome Data Viewer
    Location:
    15q22.31
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (64095982..64144231)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (61903135..61951407)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (64388181..64436430)

    Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101928988 Neighboring gene death associated protein kinase 2 Neighboring gene Sharpr-MPRA regulatory region 12240 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:64264631-64265378 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:64277639-64278140 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:64290279-64290780 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6524 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9547 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9548 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:64318331-64318496 Neighboring gene NANOG hESC enhancer GRCh37_chr15:64330918-64331419 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9549 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9550 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6525 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6526 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6527 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:64342658-64343204 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9551 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9552 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:64385112-64385674 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9554 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9556 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9555 Neighboring gene Sharpr-MPRA regulatory region 7733 Neighboring gene cytosolic iron-sulfur assembly component 2A Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9557 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9558 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9559 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:64437862-64438378 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9560 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6528 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6529 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:64445879-64446610 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9561 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:64453780-64454344 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:64454578-64455078 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:64455079-64455579 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9565 Neighboring gene sorting nexin 22 Neighboring gene casein kinase 1 gamma 1 Neighboring gene peptidylprolyl isomerase B Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:64538178-64538678 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:64538679-64539179 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9566 Neighboring gene Sharpr-MPRA regulatory region 12494 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:64618290-64619150 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:64619151-64620010 Neighboring gene small nucleolar RNA SNORA48

    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?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • MGC8664

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables cadherin binding HDA PubMed 
    enables epidermal growth factor receptor binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables insulin receptor binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables leptin receptor binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables phosphatidylinositol binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables phosphatidylinositol binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein heterodimerization activity IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein homodimerization activity IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables transferrin receptor binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in Golgi apparatus IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
     
    located_in early endosome membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in endosome IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in endosome IDA
    Inferred from Direct Assay
    more info
     
    is_active_in endosome membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in endosome membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
     
    located_in lamellipodium IEA
    Inferred from Electronic Annotation
    more info
     
    located_in lysosome IDA
    Inferred from Direct Assay
    more info
     
    located_in membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of protein-containing complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of retromer complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of retromer, tubulation complex IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    part_of retromer, tubulation complex NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in vesicle IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    sorting nexin-1
    Names
    sorting nexin 1A

    NCBI Reference Sequences (RefSeq)

    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_029708.1 RefSeqGene

      Range
      5099..53348
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001242933.2NP_001229862.1  sorting nexin-1 isoform d

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) uses an alternate splice site that causes a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (d) has a distinct and longer C-terminus, compared to isoform a.
      Source sequence(s)
      AC100840, AK128179, BX108623, DB455188
      Consensus CDS
      CCDS58371.1
      UniProtKB/TrEMBL
      Q53GY8
      Related
      ENSP00000261889.5, ENST00000261889.9
      Conserved Domains (3) summary
      cd07281
      Location:145268
      PX_SNX1; The phosphoinositide binding Phox Homology domain of Sorting Nexin 1
      pfam03700
      Location:55130
      Sorting_nexin; Sorting nexin, N-terminal domain
      cl12013
      Location:286506
      BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature
    2. NM_003099.5NP_003090.2  sorting nexin-1 isoform a

      See identical proteins and their annotated locations for NP_003090.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes isoform a.
      Source sequence(s)
      AC100840, AK291752, BX108623, DB455188
      Consensus CDS
      CCDS32266.1
      UniProtKB/Swiss-Prot
      A6NM19, A8K6T7, H0Y2M5, O60750, O60751, Q13596, Q6ZRJ8
      UniProtKB/TrEMBL
      Q53GY8
      Related
      ENSP00000453785.1, ENST00000559844.6
      Conserved Domains (3) summary
      cd07281
      Location:145268
      PX_SNX1; The phosphoinositide binding Phox Homology domain of Sorting Nexin 1
      cd07665
      Location:286519
      BAR_SNX1; The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 1
      pfam03700
      Location:1190
      Sorting_nexin; Sorting nexin, N-terminal domain
    3. NM_148955.4NP_683758.1  sorting nexin-1 isoform b

      See identical proteins and their annotated locations for NP_683758.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an in-frame segment of the 5' coding region, compared to variant 1. It encodes a shorter isoform (b), also known as SNX1A, that is missing an internal segment compared to isoform a.
      Source sequence(s)
      AC100840, AF065484, BX108623, DB455188
      Consensus CDS
      CCDS32268.1
      UniProtKB/TrEMBL
      Q53GY8
      Related
      ENSP00000453567.1, ENST00000561026.5
      Conserved Domains (2) summary
      cd07665
      Location:221454
      BAR_SNX1; The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 1
      cl02563
      Location:91203
      PX_domain; The Phox Homology domain, a phosphoinositide binding module

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000015.10 Reference GRCh38.p14 Primary Assembly

      Range
      64095982..64144231
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060939.1 Alternate T2T-CHM13v2.0

      Range
      61903135..61951407
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_152826.2: Suppressed sequence

      Description
      NM_152826.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.