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SNX10 sorting nexin 10 [ Homo sapiens (human) ]

Gene ID: 29887, updated on 19-Jun-2019

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
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

Genomic context

See SNX10 in Genome Data Viewer
Location:
7p15.2
Exon count:
12
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 7 NC_000007.14 (26291878..26374329)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (26331515..26413949)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene chromobox 3 Neighboring gene ribosomal protein L23 pseudogene 7 Neighboring gene uncharacterized LOC105375304 Neighboring gene uncharacterized LOC441204 Neighboring gene uncharacterized LOC105375202 Neighboring gene VISTA enhancer hs769

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 FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Osteopetrosis, autosomal recessive 8
MedGen: C3554478 OMIM: 615085 GeneReviews: Not available
not available

NHGRI GWAS Catalog

Description
Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women.
NHGRI GWA 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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC33054

Gene Ontology Provided by GOA

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

NCBI Reference Sequences (RefSeq)

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
    5001..87435
    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
    Q9Y5X0
    UniProtKB/TrEMBL
    A0A024RA70, B4DJM0
    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_001199837.2NP_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)
    AK296142, BC034992, BJ995940
    UniProtKB/Swiss-Prot
    Q9Y5X0
    UniProtKB/TrEMBL
    B4DJM0
    Related
    ENSP00000478710.1, ENST00000619420.4
    Conserved Domains (1) summary
    cd06898
    Location:9106
    PX_SNX10; The phosphoinositide binding Phox Homology domain of Sorting Nexin 10
  3. NM_001199838.1NP_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)
    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/Swiss-Prot
    Q9Y5X0
    UniProtKB/TrEMBL
    B4DJM0
    Related
    ENSP00000408164.1, ENST00000416246.5
    Conserved Domains (1) summary
    cd06898
    Location:38135
    PX_SNX10; The phosphoinositide binding Phox Homology domain of Sorting Nexin 10
  5. NM_001318199.2NP_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)
    AC010677, AF121860, BC031050, BU630498, DA377368
    Consensus CDS
    CCDS5399.1
    UniProtKB/Swiss-Prot
    Q9Y5X0
    UniProtKB/TrEMBL
    A0A024RA70, 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
    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
    Conserved Domains (1) summary
    cd06898
    Location:38135
    PX_SNX10; The phosphoinositide binding Phox Homology domain of Sorting Nexin 10
  8. NM_013322.2NP_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)
    BC031050, BM147978
    Consensus CDS
    CCDS5399.1
    UniProtKB/Swiss-Prot
    Q9Y5X0
    UniProtKB/TrEMBL
    A0A024RA70, Q8N5Z3
    Related
    ENSP00000343709.4, ENST00000338523.8
    Conserved Domains (1) summary
    cd06898
    Location:12109
    PX_SNX10; The phosphoinositide binding Phox Homology domain of Sorting Nexin 10

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000007.14 Reference GRCh38.p13 Primary Assembly

    Range
    26291878..26374329
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017012086.1XP_016867575.1  sorting nexin-10 isoform X1

    UniProtKB/TrEMBL
    B4DJM0
    Conserved Domains (1) summary
    cd06898
    Location:38135
    PX_SNX10; The phosphoinositide binding Phox Homology domain of Sorting Nexin 10
  2. XM_006715712.2XP_006715775.1  sorting nexin-10 isoform X2

    See identical proteins and their annotated locations for XP_006715775.1

    UniProtKB/Swiss-Prot
    Q9Y5X0
    UniProtKB/TrEMBL
    A0A024RA70
    Conserved Domains (1) summary
    cd06898
    Location:12109
    PX_SNX10; The phosphoinositide binding Phox Homology domain of Sorting Nexin 10
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