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SNX1 sorting nexin 1 [ Homo sapiens (human) ]

Gene ID: 6642, updated on 7-Apr-2024

Summary

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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
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Genomic context

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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

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. Down-regulation of SNX1 predicts poor prognosis and contributes to drug resistance in colorectal cancer. Bian Z, et al. Tumour Biol, 2016 May. PMID 26643894
  2. MicroRNA-95 promotes cell proliferation and targets sorting Nexin 1 in human colorectal carcinoma. Huang Z, et al. Cancer Res, 2011 Apr 1. PMID 21427358
  3. Sorting nexin-1 defines an early phase of Salmonella-containing vacuole-remodeling during Salmonella infection. Bujny MV, et al. J Cell Sci, 2008 Jun 15. PMID 18505799
  4. Sorting nexin 1 down-regulation promotes colon tumorigenesis. Nguyen LN, et al. Clin Cancer Res, 2006 Dec 1. PMID 17145813
  5. Endosomal localization and function of sorting nexin 1. Zhong Q, et al. Proc Natl Acad Sci U S A, 2002 May 14. PMID 11997453, Free PMC Article

See all (109) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Biochemical basis for an interaction between SNX27 and the flexible SNX1 N-terminus.
    Title: Biochemical basis for an interaction between SNX27 and the flexible SNX1 N-terminus.
  2. Sorting nexin 1 loss results in increased oxidative stress and hypertension.
    Title: Sorting nexin 1 loss results in increased oxidative stress and hypertension.
  3. Data suggest that GLP1R signaling in pancreatic beta-cells leading to insulin secretion involves interactions of GLP1R with HIP1, SNX1, and SNX27; HIP1 appears to regulate coupling of cell surface GLP1R activation with endocytosis; SNX1 and SNX27 appear to control balance between GLP1R plasma membrane recycling and lysosomal degradation.
    Title: A Targeted RNAi Screen Identifies Endocytic Trafficking Factors That Control GLP-1 Receptor Signaling in Pancreatic β-Cells.
  4. SNX1 was down-regulated in CRC and associated with poor prognosis. Our data also showed that SNX1 inhibited the proliferation of CRC cells and increased the sensitivity to the most commonly used drugs for CRC.
    Title: Down-regulation of SNX1 predicts poor prognosis and contributes to drug resistance in colorectal cancer.
  5. miR-95 functions as an oncogene role in non-small cell lung cancer cells by directly targeting SNX1.
    Title: MiR-95 induces proliferation and chemo- or radioresistance through directly targeting sorting nexin1 (SNX1) in non-small cell lung cancer.
  6. Results show that suppression of EGFR membrane recycling by SNX1 appears to be critical for the activation of EGFR /PI3K/AKT signaling pathway in human lung cancer cells.
    Title: EGF‑stimulated AKT activation is mediated by EGFR recycling via an early endocytic pathway in a gefitinib‑resistant human lung cancer cell line.
  7. we suggest that SNX1 is involved in the negative regulation of ligand-induced EGFR phosphorylation and mediates EGFR/pEGFR trafficking out of early endosomes
    Title: Silencing of SNX1 by siRNA stimulates the ligand-induced endocytosis of EGFR and increases EGFR phosphorylation in gefitinib-resistant human lung cancer cell lines.
  8. SNX1 has a crucial role in D(5)R trafficking and SNX1 depletion results in D(5)R dysfunction and thus may represent a novel mechanism for the pathogenesis of essential hypertension
    Title: Sorting nexin 1 loss results in D5 dopamine receptor dysfunction in human renal proximal tubule cells and hypertension in mice.
  9. This study found that significant evidence of association with SNX1 (VEGAS p = 0.035) in patient with Alzheimer disease.
    Title: Identification of Alzheimer disease-associated variants in genes that regulate retromer function.
  10. SNX4, but not SNX1 and SNX8, is associated with the Rab11-recycling endosomes and that a high frequency of SNX4-mediated tubule formation is observed as endosomes undergo Rab4-to-Rab11 transition.
    Title: SNX-BAR-mediated endosome tubulation is co-ordinated with endosome maturation.
Submit: New GeneRIF Correction See all GeneRIFs (25)

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

  • 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 
Process Evidence Code Pubs
involved_in early endosome to Golgi transport IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in early endosome to Golgi transport IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in intracellular protein transport IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in lamellipodium morphogenesis IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in receptor internalization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in retrograde transport, endosome to Golgi IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in retrograde transport, endosome to Golgi NAS
Non-traceable Author Statement
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

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Preferred Names
sorting nexin-1
Names
sorting nexin 1A

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_029708.1 RefSeqGene

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

mRNA and Protein(s)

  1. NM_001242933.2 → NP_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:145 → 268
    PX_SNX1; The phosphoinositide binding Phox Homology domain of Sorting Nexin 1
    pfam03700
    Location:55 → 130
    Sorting_nexin; Sorting nexin, N-terminal domain
    cl12013
    Location:286 → 506
    BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature

  2. NM_003099.5 → NP_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:145 → 268
    PX_SNX1; The phosphoinositide binding Phox Homology domain of Sorting Nexin 1
    cd07665
    Location:286 → 519
    BAR_SNX1; The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 1
    pfam03700
    Location:11 → 90
    Sorting_nexin; Sorting nexin, N-terminal domain

  3. NM_148955.4 → NP_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:221 → 454
    BAR_SNX1; The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 1
    cl02563
    Location:91 → 203
    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.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q13596.3 GenPept UniProtKB/Swiss-Prot:Q13596

Gene LinkOut

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

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