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    SNX7 sorting nexin 7 [ Homo sapiens (human) ]

    Gene ID: 51375, updated on 3-Apr-2024

    Summary

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    Official Symbol
    SNX7provided by HGNC
    Official Full Name
    sorting nexin 7provided by HGNC
    Primary source
    HGNC:HGNC:14971
    See related
    Ensembl:ENSG00000162627 MIM:614904; AllianceGenome:HGNC:14971
    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
    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 some family members, and its exact function is unknown. Alternative splicing results in multiple transcript variants. A related pseudogene has been identified on chromosome 11. [provided by RefSeq, Jun 2010]
    Expression
    Ubiquitous expression in colon (RPKM 10.6), small intestine (RPKM 8.3) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    1p21.3
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (98661319..98760500)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (98509451..98608619)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (99127277..99226056)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124900404 Neighboring gene long intergenic non-protein coding RNA 1776 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:98789036-98790235 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:98816624-98817823 Neighboring gene uncharacterized LOC124904229 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:98981623-98982822 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:99054546-99055107 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1111 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1112 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1113 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:99248941-99249530 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:99249531-99250120 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1357 Neighboring gene phospholipid phosphatase related 5 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:99469275-99470249 Neighboring gene PLPPR5 antisense RNA 1 Neighboring gene NANOG hESC enhancer GRCh37_chr1:99543443-99543978 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:99649439-99649606 Neighboring gene Sharpr-MPRA regulatory region 9288 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:99770787-99771986 Neighboring gene phospholipid phosphatase related 4

    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. Do GnRH analogues directly affect human endometrial epithelial cell gene expression? Zhang X, et al. Mol Hum Reprod, 2010 May. PMID 20203127
    2. Overexpression of SNX7 reduces Aβ production by enhancing lysosomal degradation of APP. Xu S, et al. Biochem Biophys Res Commun, 2018 Jan 1. PMID 29080748
    3. New locus for hereditary spastic paraplegia maps to chromosome 1p31.1-1p21.1. Orlacchio A, et al. Ann Neurol, 2005 Sep. PMID 16130112
    4. A heterodimeric SNX4--SNX7 SNX-BAR autophagy complex coordinates ATG9A trafficking for efficient autophagosome assembly. Antón Z, et al. J Cell Sci, 2020 Jul 15. PMID 32513819, Free PMC Article
    5. Molecular basis for SNX-BAR-mediated assembly of distinct endosomal sorting tubules. van Weering JR, et al. EMBO J, 2012 Nov 28. PMID 23085988, Free PMC Article

    See all (26) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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

    EBI GWAS Catalog

    Description
    Genome-wide association identifies nine common variants associated with fasting proinsulin levels and provides new insights into the pathophysiology of type 2 diabetes.
    EBI GWAS Catalog
    Genome-wide association scan of dental caries in the permanent dentition.
    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

    • MGC8717, DKFZp564F052

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables phosphatidylinositol binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in autophagy of mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in endocytic recycling IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in piecemeal microautophagy of the nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of autophagosome assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in reticulophagy IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in early endosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in early endosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in early endosome membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in phagophore assembly site IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    sorting nexin-7

    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.

    mRNA and Protein(s)

    1. NM_001364903.1 → NP_001351832.1  sorting nexin-7 isoform c

      Status: REVIEWED

      Source sequence(s)
      AL627442
      UniProtKB/Swiss-Prot
      A8KAF3, D3DT50, Q53FQ3, Q5VT09, Q5VT10, Q86U82, Q8WVD4, Q96FW9, Q9UNH6, Q9Y3Z7
      UniProtKB/TrEMBL
      B4DP69
      Conserved Domains (2) summary
      cd07284
      Location:32 → 147
      PX_SNX7; The phosphoinositide binding Phox Homology domain of Sorting Nexin 7
      cd07666
      Location:131 → 373
      BAR_SNX7; The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 7

    2. NM_015976.5 → NP_057060.2  sorting nexin-7 isoform a

      See identical proteins and their annotated locations for NP_057060.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
      Source sequence(s)
      AL627442
      Consensus CDS
      CCDS755.2
      UniProtKB/Swiss-Prot
      Q9UNH6
      Related
      ENSP00000304429.3, ENST00000306121.8
      Conserved Domains (2) summary
      cd07284
      Location:96 → 211
      PX_SNX7; The phosphoinositide binding Phox Homology domain of Sorting Nexin 7
      cd07666
      Location:195 → 437
      BAR_SNX7; The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 7

    3. NM_152238.4 → NP_689424.2  sorting nexin-7 isoform b

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the central coding region, compared to variant 1, resulting in an isoform (b) that is shorter than isoform a.
      Source sequence(s)
      AL627442
      Consensus CDS
      CCDS756.2
      UniProtKB/TrEMBL
      B4DP69, E9PNL2
      Related
      ENSP00000434731.1, ENST00000529992.5
      Conserved Domains (2) summary
      cd06860
      Location:96 → 214
      PX_SNX7_30_like; The phosphoinositide binding Phox Homology domain of Sorting Nexins 7 and 30
      cl12013
      Location:159 → 382
      BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature

    RNA

    1. NR_033716.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) includes an additional internal exon in the 5' region but lacks an internal exon in the 3' region, compared to variant 1. This variant is represented as non-coding because the use of the supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AL627442
      Related
      ENST00000528824.1

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      98661319..98760500
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017001425.3 → XP_016856914.1  sorting nexin-7 isoform X2

      UniProtKB/Swiss-Prot
      A8KAF3, D3DT50, Q53FQ3, Q5VT09, Q5VT10, Q86U82, Q8WVD4, Q96FW9, Q9UNH6, Q9Y3Z7
      UniProtKB/TrEMBL
      B4DP69
      Conserved Domains (2) summary
      cd07284
      Location:32 → 147
      PX_SNX7; The phosphoinositide binding Phox Homology domain of Sorting Nexin 7
      cd07666
      Location:131 → 373
      BAR_SNX7; The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 7

    2. XM_017001428.2 → XP_016856917.1  sorting nexin-7 isoform X3

      UniProtKB/TrEMBL
      B4DP69
      Conserved Domains (2) summary
      cd07284
      Location:32 → 147
      PX_SNX7; The phosphoinositide binding Phox Homology domain of Sorting Nexin 7
      cl12013
      Location:131 → 322
      BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature

    3. XM_006710677.3 → XP_006710740.2  sorting nexin-7 isoform X1

    4. XM_011541564.4 → XP_011539866.1  sorting nexin-7 isoform X2

      See identical proteins and their annotated locations for XP_011539866.1

      UniProtKB/Swiss-Prot
      A8KAF3, D3DT50, Q53FQ3, Q5VT09, Q5VT10, Q86U82, Q8WVD4, Q96FW9, Q9UNH6, Q9Y3Z7
      UniProtKB/TrEMBL
      B4DP69
      Conserved Domains (2) summary
      cd07284
      Location:32 → 147
      PX_SNX7; The phosphoinositide binding Phox Homology domain of Sorting Nexin 7
      cd07666
      Location:131 → 373
      BAR_SNX7; The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 7

    5. XM_047422248.1 → XP_047278204.1  sorting nexin-7 isoform X2

      UniProtKB/Swiss-Prot
      A8KAF3, D3DT50, Q53FQ3, Q5VT09, Q5VT10, Q86U82, Q8WVD4, Q96FW9, Q9UNH6, Q9Y3Z7

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      98509451..98608619
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054336937.1 → XP_054192912.1  sorting nexin-7 isoform X2

      UniProtKB/Swiss-Prot
      A8KAF3, D3DT50, Q53FQ3, Q5VT09, Q5VT10, Q86U82, Q8WVD4, Q96FW9, Q9UNH6, Q9Y3Z7

    2. XM_054336936.1 → XP_054192911.1  sorting nexin-7 isoform X3

    3. XM_054336931.1 → XP_054192906.1  sorting nexin-7 isoform X1

    4. XM_054336933.1 → XP_054192908.1  sorting nexin-7 isoform X4

    5. XM_054336932.1 → XP_054192907.1  sorting nexin-7 isoform X4

    6. XM_054336934.1 → XP_054192909.1  sorting nexin-7 isoform X2

      UniProtKB/Swiss-Prot
      A8KAF3, D3DT50, Q53FQ3, Q5VT09, Q5VT10, Q86U82, Q8WVD4, Q96FW9, Q9UNH6, Q9Y3Z7

    7. XM_054336935.1 → XP_054192910.1  sorting nexin-7 isoform X2

      UniProtKB/Swiss-Prot
      A8KAF3, D3DT50, Q53FQ3, Q5VT09, Q5VT10, Q86U82, Q8WVD4, Q96FW9, Q9UNH6, Q9Y3Z7
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9UNH6.1 GenPept UniProtKB/Swiss-Prot:Q9UNH6

    Gene LinkOut

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

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