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

Gene ID: 90203, updated on 2-Nov-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
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Genomic context

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See SNX21 in Genome Data Viewer
Location:
20q13.12
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (45833799..45843276)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (47570293..47579777)
RS_2024_09 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 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
  
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
  

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_2024_08

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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