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    SNX10 sorting nexin 10 [ Homo sapiens (human) ]

    Gene ID: 29887, updated on 3-Apr-2024

    Summary

    Official Symbol
    SNX10provided by HGNC
    Official Full Name
    sorting nexin 10provided by HGNC
    Primary source
    HGNC:HGNC:14974
    See related
    Ensembl:ENSG00000086300 MIM:614780; AllianceGenome:HGNC:14974
    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
    OPTB8
    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. This gene may play a role in regulating endosome homeostasis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2010]
    Expression
    Broad expression in brain (RPKM 20.5), appendix (RPKM 13.4) and 19 other tissues See more
    Orthologs
    NEW
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    Genomic context

    Location:
    7p15.2
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (26291862..26374383)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (26427536..26510069)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (26331482..26414003)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18035 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:26262791-26262893 Neighboring gene chromobox 3 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:26302097-26302746 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:26311265-26311466 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18036 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18037 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25788 Neighboring gene ribosomal protein L23 pseudogene 7 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:26341907-26342408 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:26342409-26342908 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:26375053-26375568 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:26385227-26386154 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25789 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18038 Neighboring gene SNX10 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:26437325-26438281 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18040 Neighboring gene long intergenic non-protein coding RNA 2981 Neighboring gene NANOG hESC enhancer GRCh37_chr7:26455397-26455952 Neighboring gene uncharacterized LOC105375202 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:26480672-26481247 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:26481248-26481822 Neighboring gene VISTA enhancer hs769 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:26547862-26548362 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:26548363-26548863 Neighboring gene KIAA0087 lncRNA

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Autosomal recessive osteopetrosis 8
    MedGen: C3554478 OMIM: 615085 GeneReviews: Not available
    Compare labs

    EBI GWAS Catalog

    Description
    Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women.
    EBI GWAS Catalog

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    Knockdown of sorting nexin 10 (SNX10) by shRNA library screening inhibits HIV-1 replication in cultured Jurkat T-cells PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • MGC33054

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables 1-phosphatidylinositol binding IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables ATPase binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables phosphatidylinositol 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 bone mineralization involved in bone maturation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in bone resorption IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in calcium ion homeostasis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cellular homeostasis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cellular response to leukemia inhibitory factor IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cilium assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in cilium assembly IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in endocytosis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in endosome organization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in gastric acid secretion IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in intracellular protein transport IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in osteoclast differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in protein localization to centrosome IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in protein localization to cilium IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in ruffle assembly IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in tooth eruption IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in vesicle organization IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Component Evidence Code Pubs
    located_in apical cytoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    colocalizes_with centrosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in endosome IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in extrinsic component of endosome membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in secretory granule IEA
    Inferred from Electronic Annotation
    more info
     

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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.

    Genomic

    1. NG_033902.1 RefSeqGene

      Range
      4968..87489
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001199835.1NP_001186764.1  sorting nexin-10 isoform 1

      See identical proteins and their annotated locations for NP_001186764.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes isoform 1. Variants 1, 2, and 6 encode the same isoform.
      Source sequence(s)
      AK296142, AK312850, AK316088, BC034992, BM147840, BX648363
      Consensus CDS
      CCDS5399.1
      UniProtKB/Swiss-Prot
      E9PFH5, Q8IYT5, Q9Y5X0
      UniProtKB/TrEMBL
      Q8N5Z3
      Related
      ENSP00000395474.3, ENST00000446848.6
      Conserved Domains (1) summary
      cd06898
      Location:12109
      PX_SNX10; The phosphoinositide binding Phox Homology domain of Sorting Nexin 10
    2. NM_001199837.3NP_001186766.1  sorting nexin-10 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) has a distinct 5' UTR, compared to variant 1, which results in the use of a distinct translation initiation signal. It encodes a shorter isoform (2) with a distinct N-terminus, compared to isoform 1.
      Source sequence(s)
      AC004540, AK296142, BC034992, BJ995940
      UniProtKB/TrEMBL
      Q8N5Z3
      Related
      ENST00000698092.1
      Conserved Domains (1) summary
      cd06898
      Location:9106
      PX_SNX10; The phosphoinositide binding Phox Homology domain of Sorting Nexin 10
    3. NM_001199838.2NP_001186767.1  sorting nexin-10 isoform 3

      See identical proteins and their annotated locations for NP_001186767.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) has a distinct 5' UTR, compared to variant 1, which results in the use of a downstream in-frame translation initiation signal. It encodes a shorter isoform (3), compared to isoform 1.
      Source sequence(s)
      AC004540, AK309162, BC034992, BG399132, BX648363
      Consensus CDS
      CCDS56470.1
      UniProtKB/Swiss-Prot
      Q9Y5X0
      Related
      ENSP00000386540.1, ENST00000409838.1
      Conserved Domains (1) summary
      cl02563
      Location:140
      PX_domain; The Phox Homology domain, a phosphoinositide binding module
    4. NM_001318198.1NP_001305127.1  sorting nexin-10 isoform 4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR and coding region, and uses an alternate start codon, compared to variant 1. The encoded isoform (4) has a longer N-terminus than isoform 1. Variants 4, 7 and 8 encode the same isoform (4).
      Source sequence(s)
      AK316088, BC034992, BM147840, BX648363
      UniProtKB/TrEMBL
      B4DJM0, Q8N5Z3
      Conserved Domains (1) summary
      cd06898
      Location:38135
      PX_SNX10; The phosphoinositide binding Phox Homology domain of Sorting Nexin 10
    5. NM_001318199.3NP_001305128.1  sorting nexin-10 isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) differs in the 5' UTR, compared to variant 1. Variants 1, 2, and 6 encode the same isoform (1).
      Source sequence(s)
      AC004540, AC010677, AF121860, BC031050, BU630498, DA377368
      Consensus CDS
      CCDS5399.1
      UniProtKB/Swiss-Prot
      E9PFH5, Q8IYT5, Q9Y5X0
      UniProtKB/TrEMBL
      Q8N5Z3
      Related
      ENSP00000379661.1, ENST00000396376.5
      Conserved Domains (1) summary
      cd06898
      Location:12109
      PX_SNX10; The phosphoinositide binding Phox Homology domain of Sorting Nexin 10
    6. NM_001362753.1NP_001349682.1  sorting nexin-10 isoform 4

      Status: REVIEWED

      Source sequence(s)
      AK316088, BC034992, BM147840, BX648363, DB479030
      UniProtKB/TrEMBL
      B4DJM0, Q8N5Z3
      Conserved Domains (1) summary
      cd06898
      Location:38135
      PX_SNX10; The phosphoinositide binding Phox Homology domain of Sorting Nexin 10
    7. NM_001362754.1NP_001349683.1  sorting nexin-10 isoform 4

      Status: REVIEWED

      Source sequence(s)
      AK312850, AK316088, BC034992, BM147840, BX648363
      UniProtKB/TrEMBL
      B4DJM0, Q8N5Z3
      Conserved Domains (1) summary
      cd06898
      Location:38135
      PX_SNX10; The phosphoinositide binding Phox Homology domain of Sorting Nexin 10
    8. NM_013322.3NP_037454.2  sorting nexin-10 isoform 1

      See identical proteins and their annotated locations for NP_037454.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, compared to variant 1, and encodes isoform (1). Variants 1, 2, and 6 encode the same isoform.
      Source sequence(s)
      AC004540, AC010677, AC074295
      Consensus CDS
      CCDS5399.1
      UniProtKB/Swiss-Prot
      E9PFH5, Q8IYT5, Q9Y5X0
      UniProtKB/TrEMBL
      Q8N5Z3
      Related
      ENSP00000343709.5, ENST00000338523.9
      Conserved Domains (1) summary
      cd06898
      Location:12109
      PX_SNX10; The phosphoinositide binding Phox Homology domain of Sorting Nexin 10

    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_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      26291862..26374383
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006715712.3XP_006715775.1  sorting nexin-10 isoform X2

      See identical proteins and their annotated locations for XP_006715775.1

      UniProtKB/Swiss-Prot
      E9PFH5, Q8IYT5, Q9Y5X0
      UniProtKB/TrEMBL
      Q8N5Z3
      Related
      ENST00000698091.1
      Conserved Domains (1) summary
      cd06898
      Location:12109
      PX_SNX10; The phosphoinositide binding Phox Homology domain of Sorting Nexin 10
    2. XM_047420282.1XP_047276238.1  sorting nexin-10 isoform X1

      UniProtKB/TrEMBL
      B4DJM0
    3. XM_047420283.1XP_047276239.1  sorting nexin-10 isoform X3

      UniProtKB/TrEMBL
      C9JQ16, G5E9H5
      Related
      ENSP00000387274.1, ENST00000409367.6

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      26427536..26510069
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054358026.1XP_054214001.1  sorting nexin-10 isoform X2

      UniProtKB/Swiss-Prot
      E9PFH5, Q8IYT5, Q9Y5X0
    2. XM_054358025.1XP_054214000.1  sorting nexin-10 isoform X1

      UniProtKB/TrEMBL
      B4DJM0
    3. XM_054358027.1XP_054214002.1  sorting nexin-10 isoform X3

      UniProtKB/TrEMBL
      C9JQ16, G5E9H5