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    SNX20 sorting nexin 20 [ Homo sapiens (human) ]

    Gene ID: 124460, updated on 28-Oct-2024

    Summary

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    Official Symbol
    SNX20provided by HGNC
    Official Full Name
    sorting nexin 20provided by HGNC
    Primary source
    HGNC:HGNC:30390
    See related
    Ensembl:ENSG00000167208 MIM:613281; AllianceGenome:HGNC:30390
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    SLIC1
    Summary
    SNX20 interacts with the cytoplasmic domain of PSGL1 (SELPLG; MIM 600738) and cycles PSGL1 into endosomes.[supplied by OMIM, Feb 2010]
    Expression
    Biased expression in lymph node (RPKM 7.6), appendix (RPKM 6.3) and 12 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SNX20 in Genome Data Viewer
    Location:
    16q12.1
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (50666300..50681312, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (56463916..56478923, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (50700211..50715223, complement)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903771 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7486 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7487 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:50604651-50605152 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:50605153-50605652 Neighboring gene NKD inhibitor of WNT signaling pathway 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr16:50622018-50622603 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:50631891-50632391 Neighboring gene uncharacterized LOC124903773 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:50636563-50637271 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:50640404-50641180 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr16:50643815-50644780 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:50654230-50654780 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:50654831-50655338 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:50658527-50659292 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:50659293-50660056 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10819 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:50677347-50677501 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:50680473-50680991 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:50688285-50688465 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:50699127-50699628 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10820 Neighboring gene uncharacterized LOC101927272 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10821 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7489 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10822 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10823 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10824 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10825 Neighboring gene Sharpr-MPRA regulatory region 14141 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7490 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:50743936-50744141 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10826 Neighboring gene nucleotide binding oligomerization domain containing 2 Neighboring gene Sharpr-MPRA regulatory region 1297 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10827 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7491 Neighboring gene CYLD antisense RNA 1 Neighboring gene microRNA 3181 Neighboring gene CYLD lysine 63 deubiquitinase

    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. DNA methylation-regulated SNX20 overexpression correlates with poor prognosis, immune cell infiltration, and low-grade glioma progression. Chen X, et al. Aging (Albany NY), 2022 Jun 27. PMID 35771139, Free PMC Article
    2. Chromosomal assignments of 3'-directed partial cDNA sequences representing novel genes expressed in granulocytoid cells. Murakawa K, et al. Genomics, 1994 Sep 15. PMID 7835887
    3. SLIC-1/sorting nexin 20: a novel sorting nexin that directs subcellular distribution of PSGL-1. Schaff UY, et al. Eur J Immunol, 2008 Feb. PMID 18196517, Free PMC Article
    4. Identification of molecular subtyping system and four-gene prognostic signature with immune-related genes for uveal melanoma. Xia F, et al. Exp Biol Med (Maywood), 2022 Feb. PMID 34743576, Free PMC Article
    5. Monitoring cell physiology by expression profiles and discovering cell type-specific genes by compiled expression profiles. Okubo K, et al. Genomics, 1995 Nov 20. PMID 8586417

    See all (20) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. DNA methylation-regulated SNX20 overexpression correlates with poor prognosis, immune cell infiltration, and low-grade glioma progression.
      Title: DNA methylation-regulated SNX20 overexpression correlates with poor prognosis, immune cell infiltration, and low-grade glioma progression.
    2. Identification of molecular subtyping system and four-gene prognostic signature with immune-related genes for uveal melanoma.
      Title: Identification of molecular subtyping system and four-gene prognostic signature with immune-related genes for uveal melanoma.
    3. 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.
    4. Serves as a sorting molecule that cycles P-selectin ligand protein into endosomes with no impact on leukocyte recruitment.
      Title: SLIC-1/sorting nexin 20: a novel sorting nexin that directs subcellular distribution of PSGL-1.
    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
    A genome-wide scan of Ashkenazi Jewish Crohn's disease suggests novel susceptibility loci.
    EBI GWAS Catalog
    Discovery of six new susceptibility loci and analysis of pleiotropic effects in leprosy.
    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

    • MGC35578

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables phosphatidylinositol phosphate binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables phosphatidylinositol-3-phosphate binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables phosphatidylinositol-4,5-bisphosphate binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in early endosome membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in early endosome membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    sorting nexin-20
    Names
    selectin ligand-interactor cytoplasmic 1

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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_001144972.2 → NP_001138444.1  sorting nexin-20 isoform 3

      See identical proteins and their annotated locations for NP_001138444.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses an alternative 3' exon, compared to variant 1. The resulting isoform (3) has a distinct C-terminus and is shorter than isoform 1.
      Source sequence(s)
      AK055837, AK292650, BC063423, D20065
      Consensus CDS
      CCDS45481.1
      UniProtKB/Swiss-Prot
      Q7Z614
      Related
      ENSP00000388875.2, ENST00000423026.6
      Conserved Domains (1) summary
      cl02563
      Location:76 → 94
      PX_domain; The Phox Homology domain, a phosphoinositide binding module

    2. NM_153337.3 → NP_699168.1  sorting nexin-20 isoform 2

      See identical proteins and their annotated locations for NP_699168.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternative 3' exon, compared to variant 1. The resulting isoform (2) has a distinct C-terminus and is shorter than isoform 1.
      Source sequence(s)
      AA278249, AK055837, BC063423, D20065
      Consensus CDS
      CCDS10744.1
      UniProtKB/Swiss-Prot
      Q7Z614
      Related
      ENSP00000300590.3, ENST00000300590.7
      Conserved Domains (1) summary
      cl02563
      Location:76 → 95
      PX_domain; The Phox Homology domain, a phosphoinositide binding module

    3. NM_182854.4 → NP_878274.1  sorting nexin-20 isoform 1

      See identical proteins and their annotated locations for NP_878274.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AA278249, AC007608, AY302441, BF446287
      Consensus CDS
      CCDS10745.1
      UniProtKB/Swiss-Prot
      A8K9D5, Q08E98, Q6P4H2, Q7Z614, Q8IV59
      Related
      ENSP00000332062.4, ENST00000330943.9
      Conserved Domains (1) summary
      cd07300
      Location:76 → 189
      PX_SNX20; The phosphoinositide binding Phox Homology domain of Sorting Nexin 20

    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_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      50666300..50681312 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      56463916..56478923 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q7Z614.1 GenPept UniProtKB/Swiss-Prot:Q7Z614

    Gene LinkOut

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