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    SNX12 sorting nexin 12 [ Homo sapiens (human) ]

    Gene ID: 29934, updated on 5-Mar-2024

    Summary

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    Official Symbol
    SNX12provided by HGNC
    Official Full Name
    sorting nexin 12provided by HGNC
    Primary source
    HGNC:HGNC:14976
    See related
    Ensembl:ENSG00000147164 MIM:300883; AllianceGenome:HGNC:14976
    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
    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. A similar protein in mouse may be involved in regulating the neurite outgrowth. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Jan 2012]
    Expression
    Ubiquitous expression in kidney (RPKM 19.5), thyroid (RPKM 17.8) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SNX12 in Genome Data Viewer
    Location:
    Xq13.1
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (71059247..71073426, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (69493335..69507559, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (70279097..70293276, complement)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene RNA, U1 small nuclear 56, pseudogene Neighboring gene suppressor of cytokine signaling 5 pseudogene 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29734 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29735 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:70288147-70288340 Neighboring gene Sharpr-MPRA regulatory region 4327 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:70320272-70320882 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29736 Neighboring gene forkhead box O4 Neighboring gene chromosome X open reading frame 65

    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. Essential and selective role of SNX12 in transport of endocytic and retrograde cargo. Priya A, et al. J Cell Sci, 2017 Aug 15. PMID 28705836
    2. Sorting nexin 12 interacts with BACE1 and regulates BACE1-mediated APP processing. Zhao Y, et al. Mol Neurodegener, 2012 Jun 18. PMID 22709416, Free PMC Article
    3. Expression of sorting nexin 12 is regulated in developing cerebral cortical neurons. Mizutani R, et al. J Neurosci Res, 2012 Apr. PMID 22109349
    4. SNX12 role in endosome membrane transport. Pons V, et al. PLoS One, 2012. PMID 22719997, Free PMC Article
    5. The role of metallothionein in the pathogenesis of acute lung injury. Wesselkamper SC, et al. Am J Respir Cell Mol Biol, 2006 Jan. PMID 16166738, Free PMC Article

    See all (29) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SNX12 plays a key role in intraluminal vesicle formation and in the maturation of a subpopulation of early endosomes into late endosomes, thereby regulating selective endocytic transport of cargo for degradation.
      Title: Essential and selective role of SNX12 in transport of endocytic and retrograde cargo.
    2. SNX12 protein level is dramatically decreased in the brain of Alzheimer's disease patients as compared to that of controls.
      Title: Sorting nexin 12 interacts with BACE1 and regulates BACE1-mediated APP processing.
    3. find that overexpression of SNX12 restores the sorting process in an Hrs knockdown background. Altogether, our data show that despite lower expression level, SNX12 shares redundant functions with SNX3 in the biogenesis of multivesicular endosomes
      Title: SNX12 role in endosome membrane transport.
    4. Metallothionein deficient mice have a marked decrease in Snx12 during acute lung injury
      Title: The role of metallothionein in the pathogenesis of acute lung injury.
    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

    • FLJ22128, MGC118982, MGC118983

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables enzyme binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables phosphatidylinositol binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables phosphatidylinositol-3-phosphate binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in endocytic recycling IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in late endosome to Golgi transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of early endosome to late endosome transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of protein catabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of protein processing IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of protein transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of endocytosis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in early endosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in early endosome membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of retromer complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    sorting nexin-12

    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_001256185.2 → NP_001243114.1  sorting nexin-12 isoform 1

      See identical proteins and their annotated locations for NP_001243114.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1). Both variants 1 and 2 encode the same isoform (1).
      Source sequence(s)
      AL590764, BC024301, DA736880
      Consensus CDS
      CCDS14405.1
      UniProtKB/Swiss-Prot
      F8W8K5, Q8WUG9, Q9UMY4
      UniProtKB/TrEMBL
      A0A087X0R6, Q3SYF1
      Related
      ENSP00000481314.1, ENST00000622277.4
      Conserved Domains (1) summary
      cd07294
      Location:27 → 158
      PX_SNX12; The phosphoinositide binding Phox Homology domain of Sorting Nexin 12

    2. NM_001256186.2 → NP_001243115.1  sorting nexin-12 isoform 2

      See identical proteins and their annotated locations for NP_001243115.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) has multiple coding region differences, compared to variant 1, one of which results in a frameshift. The resulting protein (isoform 2) has a distinct C-terminus and is shorter than isoform 1.
      Source sequence(s)
      AL590764, BC024301, DA847821
      Conserved Domains (1) summary
      cl02563
      Location:27 → 83
      PX_domain; The Phox Homology domain, a phosphoinositide binding module

    3. NM_001256187.2 → NP_001243116.1  sorting nexin-12 isoform 3

      See identical proteins and their annotated locations for NP_001243116.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks an exon in the coding region which results in a frameshift, compared to variant 1. The resulting protein (isoform 3) has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AL590764, BC024301, DB251077
      Conserved Domains (1) summary
      cl02563
      Location:27 → 87
      PX_domain; The Phox Homology domain, a phosphoinositide binding module

    4. NM_001256188.2 → NP_001243117.1  sorting nexin-12 isoform 4

      See identical proteins and their annotated locations for NP_001243117.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. This results in a shorter protein (isoform 4), compared to isoform 1.
      Source sequence(s)
      AL590764, BC024301, DA439434
      Consensus CDS
      CCDS59169.1
      UniProtKB/TrEMBL
      A0A087X0R6
      Related
      ENSP00000276105.3, ENST00000276105.3
      Conserved Domains (1) summary
      cl02563
      Location:27 → 154
      PX_domain; The Phox Homology domain, a phosphoinositide binding module

    5. NM_013346.4 → NP_037478.2  sorting nexin-12 isoform 1

      See identical proteins and their annotated locations for NP_037478.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and represents use of an alternate promoter, compared to variant 1. Both variants 1 and 2 encode the same isoform (1).
      Source sequence(s)
      AL590764, BC024301, BC103847
      Consensus CDS
      CCDS14405.1
      UniProtKB/Swiss-Prot
      F8W8K5, Q8WUG9, Q9UMY4
      UniProtKB/TrEMBL
      A0A087X0R6, Q3SYF1
      Related
      ENSP00000363392.3, ENST00000374274.8
      Conserved Domains (1) summary
      cd07294
      Location:27 → 158
      PX_SNX12; The phosphoinositide binding Phox Homology domain of Sorting Nexin 12

    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_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      71059247..71073426 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047442038.1 → XP_047297994.1  sorting nexin-12 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      69493335..69507559 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9UMY4.4 GenPept UniProtKB/Swiss-Prot:Q9UMY4

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