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    SNX13 sorting nexin 13 [ Homo sapiens (human) ]

    Gene ID: 23161, updated on 3-Nov-2024

    Summary

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    Official Symbol
    SNX13provided by HGNC
    Official Full Name
    sorting nexin 13provided by HGNC
    Primary source
    HGNC:HGNC:21335
    See related
    Ensembl:ENSG00000071189 MIM:606589; AllianceGenome:HGNC:21335
    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
    RGS-PX1
    Summary
    This gene encodes a PHOX domain- and RGS domain-containing protein that belongs to the sorting nexin (SNX) family and the regulator of G protein signaling (RGS) family. The PHOX domain is a phosphoinositide binding domain, and the SNX family members are involved in intracellular trafficking. The RGS family members are regulatory molecules that act as GTPase activating proteins for G alpha subunits of heterotrimeric G proteins. The RGS domain of this protein interacts with G alpha(s), accelerates its GTP hydrolysis, and attenuates G alpha(s)-mediated signaling. Overexpression of this protein delayes lysosomal degradation of the epidermal growth factor receptor. Because of its bifunctional role, this protein may link heterotrimeric G protein signaling and vesicular trafficking. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in thyroid (RPKM 8.8), testis (RPKM 6.4) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SNX13 in Genome Data Viewer
    Location:
    7p21.1
    Exon count:
    31
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (17790761..17940494, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (17920498..18070184, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (17830385..17980117, complement)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2888 Neighboring gene uncharacterized LOC105375172 Neighboring gene long intergenic non-protein coding RNA 2889 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17986 Neighboring gene Sharpr-MPRA regulatory region 7324 Neighboring gene NANOG hESC enhancer GRCh37_chr7:17638482-17638983 Neighboring gene NANOG hESC enhancer GRCh37_chr7:17702244-17702762 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25675 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25676 Neighboring gene Sharpr-MPRA regulatory region 6645 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:17864406-17864592 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:17960890-17961390 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:18017138-18017327 Neighboring gene MRM3 pseudogene 2 Neighboring gene phosphoribosyl pyrophosphate synthetase 1 like 1

    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 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. CRISPR screens for lipid regulators reveal a role for ER-bound SNX13 in lysosomal cholesterol export. Lu A, et al. J Cell Biol, 2022 Feb 7. PMID 34936700, Free PMC Article
    2. RGS-PX1, a GAP for GalphaS and sorting nexin in vesicular trafficking. Zheng B, et al. Science, 2001 Nov 30. PMID 11729322
    3. Identification and characterisation of the gene TWIST NEIGHBOR (TWISTNB) located in the microdeletion syndrome 7p21 region. Kosan C, et al. Cytogenet Genome Res, 2002. PMID 12438708
    4. Structural basis for different phosphoinositide specificities of the PX domains of sorting nexins regulating G-protein signaling. Mas C, et al. J Biol Chem, 2014 Oct 10. PMID 25148684, Free PMC Article
    5. Sorting out the cellular functions of sorting nexins. Worby CA, et al. Nat Rev Mol Cell Biol, 2002 Dec. PMID 12461558

    See all (24) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. CRISPR screens for lipid regulators reveal a role for ER-bound SNX13 in lysosomal cholesterol export.
      Title: CRISPR screens for lipid regulators reveal a role for ER-bound SNX13 in lysosomal cholesterol export.
    2. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    Submit: New GeneRIF Correction

    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
    Discovery and refinement of loci associated with lipid levels.
    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

    • KIAA0713

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables phosphatidylinositol binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables phosphatidylinositol binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables phosphatidylinositol-3-phosphate binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in intracellular protein transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of signal transduction IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of GTPase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in early endosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in early endosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in early endosome membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    sorting nexin-13
    Names
    rgs domain- and phox domain-containing protein

    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_001350862.2 → NP_001337791.1  sorting nexin-13 isoform a

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (a).
      Source sequence(s)
      AC073205, AC080080
      UniProtKB/Swiss-Prot
      B2RCI9, O94821, Q8WVZ2, Q8WXH8, Q9Y5W8
      UniProtKB/TrEMBL
      Q86XC4
      Related
      ENSP00000479044.1, ENST00000611725.4
      Conserved Domains (4) summary
      cd06873
      Location:557 → 687
      PX_SNX13; The phosphoinositide binding Phox Homology domain of Sorting Nexin 13
      cd08719
      Location:377 → 511
      RGS_SNX13; Regulator of G protein signaling (RGS) domain found in the Sorting Nexin 13 (SNX13) protein
      smart00313
      Location:97 → 284
      PXA; Domain associated with PX domains
      pfam08628
      Location:803 → 911
      Nexin_C; Sorting nexin C terminal

    2. NM_001350863.2 → NP_001337792.1  sorting nexin-13 isoform c

      Status: REVIEWED

      Source sequence(s)
      AC073205, AC080080
      UniProtKB/TrEMBL
      Q86XC4
      Conserved Domains (4) summary
      cd06873
      Location:477 → 596
      PX_SNX13; The phosphoinositide binding Phox Homology domain of Sorting Nexin 13
      cd08719
      Location:297 → 431
      RGS_SNX13; Regulator of G protein signaling (RGS) domain found in the Sorting Nexin 13 (SNX13) protein
      smart00313
      Location:17 → 204
      PXA; Domain associated with PX domains
      pfam08628
      Location:712 → 820
      Nexin_C; Sorting nexin C terminal

    3. NM_001350864.2 → NP_001337793.1  sorting nexin-13 isoform d

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4), encodes isoform d.
      Source sequence(s)
      AC073205, AC080080
      UniProtKB/TrEMBL
      Q86XC4
      Conserved Domains (4) summary
      cd06873
      Location:455 → 574
      PX_SNX13; The phosphoinositide binding Phox Homology domain of Sorting Nexin 13
      cd08719
      Location:275 → 409
      RGS_SNX13; Regulator of G protein signaling (RGS) domain found in the Sorting Nexin 13 (SNX13) protein
      pfam08628
      Location:690 → 798
      Nexin_C; Sorting nexin C terminal
      cl02564
      Location:45 → 182
      PXA; PXA domain

    4. NM_001350866.2 → NP_001337795.1  sorting nexin-13 isoform e

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6), as well as variant 7, encodes isoform e.
      Source sequence(s)
      AC073205, AC080080
      UniProtKB/TrEMBL
      B3KN60
      Conserved Domains (4) summary
      cd06873
      Location:354 → 473
      PX_SNX13; The phosphoinositide binding Phox Homology domain of Sorting Nexin 13
      cd08719
      Location:174 → 308
      RGS_SNX13; Regulator of G protein signaling (RGS) domain found in the Sorting Nexin 13 (SNX13) protein
      pfam08628
      Location:589 → 697
      Nexin_C; Sorting nexin C terminal
      cl02564
      Location:13 → 81
      PXA; PXA domain

    5. NM_001350867.2 → NP_001337796.1  sorting nexin-13 isoform e

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7), as well as variant 6, encodes isoform e.
      Source sequence(s)
      AC073205, AC080080
      UniProtKB/TrEMBL
      B3KN60
      Conserved Domains (4) summary
      cd06873
      Location:354 → 473
      PX_SNX13; The phosphoinositide binding Phox Homology domain of Sorting Nexin 13
      cd08719
      Location:174 → 308
      RGS_SNX13; Regulator of G protein signaling (RGS) domain found in the Sorting Nexin 13 (SNX13) protein
      pfam08628
      Location:589 → 697
      Nexin_C; Sorting nexin C terminal
      cl02564
      Location:13 → 81
      PXA; PXA domain

    6. NM_001350868.2 → NP_001337797.1  sorting nexin-13 isoform f

      Status: REVIEWED

      Source sequence(s)
      AC073205, AC080080
      Conserved Domains (2) summary
      cd08719
      Location:377 → 511
      RGS_SNX13; Regulator of G protein signaling (RGS) domain found in the Sorting Nexin 13 (SNX13) protein
      smart00313
      Location:97 → 284
      PXA; Domain associated with PX domains

    7. NM_001350870.2 → NP_001337799.1  sorting nexin-13 isoform g

      Status: REVIEWED

      Source sequence(s)
      AC073205, AC080080
      Consensus CDS
      CCDS87483.1
      UniProtKB/TrEMBL
      Q9NSH0
      Related
      ENSP00000386639.1, ENST00000409604.1
      Conserved Domains (1) summary
      cl02564
      Location:97 → 149
      PXA; PXA domain

    8. NM_015132.5 → NP_055947.1  sorting nexin-13 isoform b

      See identical proteins and their annotated locations for NP_055947.1

      Status: REVIEWED

      Source sequence(s)
      AC073205, AF420470, BC045667, DB050735
      Consensus CDS
      CCDS47551.1
      UniProtKB/TrEMBL
      Q86XC4
      Related
      ENSP00000398789.2, ENST00000428135.7
      Conserved Domains (4) summary
      cd06873
      Location:557 → 676
      PX_SNX13; The phosphoinositide binding Phox Homology domain of Sorting Nexin 13
      cd08719
      Location:377 → 511
      RGS_SNX13; Regulator of G protein signaling (RGS) domain found in the Sorting Nexin 13 (SNX13) protein
      smart00313
      Location:97 → 284
      PXA; Domain associated with PX domains
      pfam08628
      Location:792 → 900
      Nexin_C; Sorting nexin C terminal

    RNA

    1. NR_146932.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC073205, AC080080

    2. NR_146933.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC073205, AC080080

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      17790761..17940494 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017011893.3 → XP_016867382.1  sorting nexin-13 isoform X2

      UniProtKB/TrEMBL
      Q86XC4

    2. XM_011515229.3 → XP_011513531.1  sorting nexin-13 isoform X1

      UniProtKB/TrEMBL
      Q86XC4
      Conserved Domains (4) summary
      cd06873
      Location:557 → 687
      PX_SNX13; The phosphoinositide binding Phox Homology domain of Sorting Nexin 13
      cd08719
      Location:377 → 511
      RGS_SNX13; Regulator of G protein signaling (RGS) domain found in the Sorting Nexin 13 (SNX13) protein
      smart00313
      Location:97 → 284
      PXA; Domain associated with PX domains
      pfam08628
      Location:749 → 857
      Nexin_C; Sorting nexin C terminal

    3. XM_047420073.1 → XP_047276029.1  sorting nexin-13 isoform X3

    4. XM_047420074.1 → XP_047276030.1  sorting nexin-13 isoform X4

    5. XM_047420075.1 → XP_047276031.1  sorting nexin-13 isoform X5

    6. XM_005249673.6 → XP_005249730.1  sorting nexin-13 isoform X6

      Conserved Domains (2) summary
      cd08719
      Location:377 → 511
      RGS_SNX13; Regulator of G protein signaling (RGS) domain found in the Sorting Nexin 13 (SNX13) protein
      smart00313
      Location:97 → 284
      PXA; Domain associated with PX domains

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      17920498..18070184 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054357672.1 → XP_054213647.1  sorting nexin-13 isoform X2

    2. XM_054357671.1 → XP_054213646.1  sorting nexin-13 isoform X1

    3. XM_054357673.1 → XP_054213648.1  sorting nexin-13 isoform X3

    4. XM_054357674.1 → XP_054213649.1  sorting nexin-13 isoform X4

    5. XM_054357675.1 → XP_054213650.1  sorting nexin-13 isoform X5

    6. XM_054357676.1 → XP_054213651.1  sorting nexin-13 isoform X6

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Y5W8.4 GenPept UniProtKB/Swiss-Prot:Q9Y5W8

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