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SNX20 sorting nexin 20 [ Homo sapiens (human) ]

Gene ID: 124460, updated on 17-Jun-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
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (50666300..50681312, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (56463916..56478923, complement)
105.20220307 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
  • 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 (19) 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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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_2023_10

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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