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SNX13 sorting nexin 13 [ Homo sapiens (human) ]

Gene ID: 23161, updated on 3-Apr-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
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (17790761..17940494, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (17920498..18070184, complement)
105.20220307 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
  • 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. 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
  3. RGS-PX1, a GAP for GalphaS and sorting nexin in vesicular trafficking. Zheng B, et al. Science, 2001 Nov 30. PMID 11729322
  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 (22) 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_2023_10

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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