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SNX12 sorting nexin 12 [ Homo sapiens (human) ]

Gene ID: 29934, updated on 4-Jan-2025

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_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (71059247..71073426, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (69493335..69507559, complement)
RS_2024_09 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: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 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 (30) 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)

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_2024_08

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

Gene LinkOut

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