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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
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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

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