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    SNX21 sorting nexin family member 21 [ Homo sapiens (human) ]

    Gene ID: 90203, updated on 3-Apr-2024

    Summary

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    Official Symbol
    SNX21provided by HGNC
    Official Full Name
    sorting nexin family member 21provided by HGNC
    Primary source
    HGNC:HGNC:16154
    See related
    Ensembl:ENSG00000124104 MIM:619200; AllianceGenome:HGNC:16154
    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
    SNXL; SNX-L; PP3993; C20orf161; dJ337O18.4
    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 does not contain a coiled coil region, like some family members. The specific function of this protein has not been determined. Multiple transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in skin (RPKM 12.2), fat (RPKM 8.5) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    20q13.12
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (45833799..45843276)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (47570293..47579777)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (44462438..44471915)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:44447254-44447902 Neighboring gene ubiquitin conjugating enzyme E2 C Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:44449199-44449846 Neighboring gene troponin C2, fast skeletal type Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12963 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12964 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12965 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:44468841-44469394 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:44470503-44471055 Neighboring gene acyl-CoA thioesterase 8 Neighboring gene MPRA-validated peak4224 silencer Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:44482305-44482834 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:44482835-44483364 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:44483365-44483894 Neighboring gene zinc finger SWIM-type containing 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17952 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17953 Neighboring gene zinc finger SWIM-type containing 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. Expression of a novel member of sorting nexin gene family, SNX-L, in human liver development. Zeng W, et al. Biochem Biophys Res Commun, 2002 Dec 13. PMID 12459172
    2. Sorting nexin-21 is a scaffold for the endosomal recruitment of huntingtin. Danson CM, et al. J Cell Sci, 2018 Sep 10. PMID 30072438, Free PMC Article
    3. The Phox homology (PX) domain, a new player in phosphoinositide signalling. Xu Y, et al. Biochem J, 2001 Dec 15. PMID 11736640, Free PMC Article
    4. Sorting out the cellular functions of sorting nexins. Worby CA, et al. Nat Rev Mol Cell Biol, 2002 Dec. PMID 12461558
    5. A large family of endosome-localized proteins related to sorting nexin 1. Teasdale RD, et al. Biochem J, 2001 Aug 15. PMID 11485546, Free PMC Article

    See all (19) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The N-terminal extension of SNX21 interacts with huntingtin and recruit Htt to an endosomal population.
      Title: Sorting nexin-21 is a scaffold for the endosomal recruitment of huntingtin.
    2. Data suggest that human sorting nexin-L (SNX-L) may be a regulatory gene involved in receptor protein degradation during embryonic liver development.
      Title: Expression of a novel member of sorting nexin gene family, SNX-L, in human liver development.
    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

    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

    • MGC29895

    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
    		  
    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
    		  

    General protein information

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    Preferred Names
    sorting nexin-21
    Names
    sorting nexin L

    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_001042632.3 → NP_001036097.1  sorting nexin-21 isoform c

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate splice site in the coding region, compared to variant 1, that results in a frameshift. The resulting isoform (c) has a shorter and distinct C-terminus that lacks a PX domain, compared to isoform a.
      Source sequence(s)
      AK095851, AL008726, BC012904, KF456922
      UniProtKB/TrEMBL
      Q5JZH4
      Related
      ENST00000344780.4
      Conserved Domains (1) summary
      cl02563
      Location:131 → 146
      PX_domain; The Phox Homology domain, a phosphoinositide binding module

    2. NM_001042633.3 → NP_001036098.1  sorting nexin-21 isoform d

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) includes an alternate exon in the 3' coding region, compared to variant 1, that results in a frameshift. The resulting isoform (d) has a shorter and distinct C-terminus that lacks a PX domain, compared to isoform a.
      Source sequence(s)
      AL008726, BM925584, DA053179, KF456922
      Consensus CDS
      CCDS42883.1
      UniProtKB/TrEMBL
      A0A0S2Z632, Q5JZH4
      Related
      ENSP00000420169.1, ENST00000462307.5
      Conserved Domains (1) summary
      cl02563
      Location:131 → 149
      PX_domain; The Phox Homology domain, a phosphoinositide binding module

    3. NM_033421.4 → NP_219489.1  sorting nexin-21 isoform a

      See identical proteins and their annotated locations for NP_219489.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform a.
      Source sequence(s)
      AL008726, KF456922
      Consensus CDS
      CCDS13377.1
      UniProtKB/Swiss-Prot
      Q5JZH5, Q5JZH6, Q5JZH7, Q8WUR6, Q969T3, Q9BR16
      UniProtKB/TrEMBL
      Q5JZH3
      Related
      ENSP00000418593.1, ENST00000491381.6
      Conserved Domains (3) summary
      cd07301
      Location:131 → 242
      PX_SNX21; The phosphoinositide binding Phox Homology domain of Sorting Nexin 21
      sd00006
      Location:244 → 268
      TPR; TPR repeat [structural motif]
      pfam13424
      Location:247 → 312
      TPR_12; Tetratricopeptide repeat

    4. NM_152897.3 → NP_690857.1  sorting nexin-21 isoform b

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks a segment of the coding region, which leads to a frameshift, compared to variant 1. The resulting isoform (b) has a shorter and distinct C-terminus that lacks a PX domain, compared to isoform a.
      Source sequence(s)
      AL008726, KF456922
      Consensus CDS
      CCDS13376.1
      UniProtKB/TrEMBL
      A0A0S2Z5T2
      Related
      ENSP00000344586.5, ENST00000342644.9
      Conserved Domains (1) summary
      cl02563
      Location:131 → 196
      PX_domain; The Phox Homology domain, a phosphoinositide binding module

    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_000020.11 Reference GRCh38.p14 Primary Assembly

      Range
      45833799..45843276
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047440581.1 → XP_047296537.1  sorting nexin-21 isoform X5

      UniProtKB/TrEMBL
      Q05DJ0
      Related
      ENSP00000478395.1, ENST00000614929.4

    2. XM_011529096.3 → XP_011527398.1  sorting nexin-21 isoform X3

      Conserved Domains (2) summary
      pfam13900
      Location:161 → 184
      GVQW; Putative domain of unknown function
      cl02563
      Location:131 → 147
      PX_domain; The Phox Homology domain, a phosphoinositide binding module

    3. XM_047440580.1 → XP_047296536.1  sorting nexin-21 isoform X4

    4. XM_011529095.3 → XP_011527397.1  sorting nexin-21 isoform X2

      UniProtKB/TrEMBL
      Q8WY78
      Conserved Domains (3) summary
      sd00006
      Location:96 → 120
      TPR; TPR repeat [structural motif]
      pfam13424
      Location:99 → 164
      TPR_12; Tetratricopeptide repeat
      cl02563
      Location:1 → 94
      PX_domain; The Phox Homology domain, a phosphoinositide binding module

    5. XM_005260608.5 → XP_005260665.1  sorting nexin-21 isoform X1

      Conserved Domains (3) summary
      sd00006
      Location:146 → 170
      TPR; TPR repeat [structural motif]
      pfam13424
      Location:149 → 214
      TPR_12; Tetratricopeptide repeat
      cl02563
      Location:37 → 144
      PX_domain; The Phox Homology domain, a phosphoinositide binding module

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060944.1 Alternate T2T-CHM13v2.0

      Range
      47570293..47579777
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054324202.1 → XP_054180177.1  sorting nexin-21 isoform X5

      UniProtKB/TrEMBL
      Q05DJ0

    2. XM_054324200.1 → XP_054180175.1  sorting nexin-21 isoform X3

    3. XM_054324201.1 → XP_054180176.1  sorting nexin-21 isoform X4

    4. XM_054324199.1 → XP_054180174.1  sorting nexin-21 isoform X2

    5. XM_054324198.1 → XP_054180173.1  sorting nexin-21 isoform X6

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q969T3.1 GenPept UniProtKB/Swiss-Prot:Q969T3

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