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SNX6 sorting nexin 6 [ Homo sapiens (human) ]

Gene ID: 58533, updated on 15-Apr-2019

Summary

Official Symbol
SNX6provided by HGNC
Official Full Name
sorting nexin 6provided by HGNC
Primary source
HGNC:HGNC:14970
See related
Ensembl:ENSG00000129515 MIM:606098
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
TFAF2; MSTP010
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 associates with the long isoform of the leptin receptor, the transforming growth factor-beta family of receptor serine-threonine kinases, and with receptor tyrosine kinases for platelet-derived growth factor, insulin, and epidermal growth factor. This protein may form oligomeric complexes with family member proteins through interactions of both the PX domain and the coiled coil regions of the molecules. Translocation of this protein from the cytoplasm to the nucleus occurs after binding to proviral integration site 1 protein. This gene results in two transcripts encoding two distinct isoforms. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in placenta (RPKM 36.9), duodenum (RPKM 33.6) and 25 other tissues See more
Orthologs

Genomic context

See SNX6 in Genome Data Viewer
Location:
14q13.1
Exon count:
14
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 14 NC_000014.9 (34561093..34630183, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (35030615..35099366, complement)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene nonconserved acetylation island sequence 117a enhancer Neighboring gene uncharacterized LOC105370449 Neighboring gene RNA, U1 small nuclear 27, pseudogene Neighboring gene nonconserved acetylation island sequence 117b enhancer Neighboring gene RNA, U1 small nuclear 28, pseudogene Neighboring gene ribosomal protein S19 pseudogene 3 Neighboring gene RNA, U6 small nuclear 1261, pseudogene Neighboring gene uncharacterized LOC107984628 Neighboring gene ribosomal protein L23a pseudogene 8

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 FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
A possible mechanism behind autoimmune disorders discovered by genome-wide linkage and association analysis in celiac disease.
NHGRI GWA Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Nef nef Genome-wide shRNA screening identifies SNX6, which is required for HIV-1 Nef-induced downregulation of CD4 in HeLa CD4+ cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Endocytosis, organism-specific biosystem (from KEGG)
    Endocytosis, organism-specific biosystemEndocytosis is a mechanism for cells to remove ligands, nutrients, and plasma membrane (PM) proteins, and lipids from the cell surface, bringing them into the cell interior. Transmembrane proteins en...
  • Endocytosis, conserved biosystem (from KEGG)
    Endocytosis, conserved biosystemEndocytosis is a mechanism for cells to remove ligands, nutrients, and plasma membrane (PM) proteins, and lipids from the cell surface, bringing them into the cell interior. Transmembrane proteins en...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC3157

Gene Ontology Provided by GOA

Function Evidence Code Pubs
dynactin binding IDA
Inferred from Direct Assay
more info
PubMed 
phosphatidylinositol binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein heterodimerization activity NAS
Non-traceable Author Statement
more info
PubMed 
protein homodimerization activity IPI
Inferred from Physical Interaction
more info
PubMed 
Component Evidence Code Pubs
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytosol IEA
Inferred from Electronic Annotation
more info
 
early endosome membrane IDA
Inferred from Direct Assay
more info
PubMed 
nucleus IEA
Inferred from Electronic Annotation
more info
 
retromer complex IDA
Inferred from Direct Assay
more info
PubMed 
retromer, tubulation complex NAS
Non-traceable Author Statement
more info
PubMed 
tubular endosome IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
sorting nexin-6
Names
TRAF4-associated factor 2
tumor necrosis factor receptor-associated factor 4(TRAF4)-associated factor 2

NCBI Reference Sequences (RefSeq)

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_001366519.1NP_001353448.1  sorting nexin-6 isoform c

    Status: REVIEWED

    Source sequence(s)
    AL445363, AL445883
    Conserved Domains (2) summary
    cl02563
    Location:30133
    PX_domain; The Phox Homology domain, a phosphoinositide binding module
    cl12013
    Location:149366
    BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature
  2. NM_021249.5NP_067072.3  sorting nexin-6 isoform a

    See identical proteins and their annotated locations for NP_067072.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) retains an intron in the 5' UTR and represents the longest transcript. The resulting isoform (a) has a shorter N-terminus compared to isoform b.
    Source sequence(s)
    AF121856, AI446034, AK124315, AL445883, BC001798, BI870378, DB021488
    Consensus CDS
    CCDS9648.1
    UniProtKB/Swiss-Prot
    Q9UNH7
    Related
    ENSP00000379779.3, ENST00000396526.7
    Conserved Domains (2) summary
    cl02563
    Location:154
    PX_domain; The Phox Homology domain, a phosphoinositide binding module
    cl12013
    Location:70287
    BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature
  3. NM_152233.4NP_689419.3  sorting nexin-6 isoform b

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) encodes the longest isoform (b).
    Source sequence(s)
    AF121856, AI446034, AK124315, BI870378, DB021488, U83194
    Consensus CDS
    CCDS41942.1
    Related
    ENSP00000498872.1, ENST00000652385.1
    Conserved Domains (2) summary
    cd07292
    Location:30170
    PX_SNX6; The phosphoinositide binding Phox Homology domain of Sorting Nexin 6
    cd07662
    Location:186403
    BAR_SNX6; The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 6

RNA

  1. NR_159357.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL445363, AL445883
  2. NR_159358.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL445363, AL445883

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000014.9 Reference GRCh38.p12 Primary Assembly

    Range
    34561093..34630183 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006720224.1XP_006720287.1  sorting nexin-6 isoform X1

RNA

  1. XR_001750486.1 RNA Sequence

  2. XR_001750485.2 RNA Sequence

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