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Protein

Sorting nexin-10

Gene

SNX10

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Probable phosphoinositide-binding protein involved in protein sorting and membrane trafficking in endosomes. Plays a role in cilium biogenesis through regulation of the transport and the localization of proteins to the cilium. Required for the localization to the cilium of V-ATPase subunit ATP6V1D and ATP6V0D1, and RAB8A. Involved in osteoclast differentiation and therefore bone resorption.3 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei53Phosphatidylinositol 3-phosphateCurated1
Binding sitei79Phosphatidylinositol 3-phosphateCurated1
Binding sitei94Phosphatidylinositol 3-phosphateCurated1

GO - Molecular functioni

  • 1-phosphatidylinositol binding Source: UniProtKB
  • ATPase binding Source: UniProtKB

GO - Biological processi

  • cilium assembly Source: UniProtKB
  • endocytosis Source: GO_Central
  • endosome organization Source: UniProtKB
  • osteoclast differentiation Source: UniProtKB
  • protein localization to centrosome Source: UniProtKB
  • protein localization to cilium Source: UniProtKB
  • protein transport Source: UniProtKB-KW
  • vesicle organization Source: GO_Central
Complete GO annotation...

Keywords - Biological processi

Cilium biogenesis/degradation, Protein transport, Transport

Keywords - Ligandi

Lipid-binding

Enzyme and pathway databases

BioCyciZFISH:ENSG00000086300-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Sorting nexin-10
Gene namesi
Name:SNX10
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 7

Organism-specific databases

HGNCiHGNC:14974. SNX10.

Subcellular locationi

GO - Cellular componenti

  • endoplasmic reticulum Source: UniProtKB
  • extrinsic component of endosome membrane Source: UniProtKB
  • microtubule organizing center Source: UniProtKB-SubCell
  • nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Cytoskeleton, Endosome, Membrane

Pathology & Biotechi

Involvement in diseasei

Osteopetrosis, autosomal recessive 8 (OPTB8)3 Publications
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA rare genetic disease characterized by abnormally dense bone, due to defective resorption of immature bone. Osteopetrosis occurs in two forms: a severe autosomal recessive form occurring in utero, infancy, or childhood, and a benign autosomal dominant form occurring in adolescence or adulthood. Recessive osteopetrosis commonly manifests in early infancy with macrocephaly, feeding difficulties, evolving blindness and deafness, bone marrow failure, severe anemia, and hepatosplenomegaly. Deafness and blindness are generally thought to represent effects of pressure on nerves. OPTB8 is clinically characterized by dense bones with no distinction between outer and inner plates, due to extensive encroachment of cortical bone into the medullary space, increased head circumference, broad open fontanelle, frontal bossing, and hepatosplenomegaly. Osteoclasts number is low and their bone resorptive capacity is impaired.
See also OMIM:615085
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_06929916R → L in OPTB8. 1 PublicationCorresponds to variant rs779298714dbSNPEnsembl.1
Natural variantiVAR_06930032Y → S in OPTB8. 1 PublicationCorresponds to variant rs771038257dbSNPEnsembl.1
Natural variantiVAR_06930151R → P in OPTB8. 1 Publication1
Natural variantiVAR_06930251R → Q in OPTB8; increased expression, produces extensive cytoplasmic vacuolation and impairs bone resorptive function. 1 PublicationCorresponds to variant rs398123011dbSNPEnsembl.1

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi53R → A: Abolishes vacuolization induced by overexpression. 1 Publication1
Mutagenesisi79K → A: Slightly reduced vacuolization induced by overexpression. 1 Publication1
Mutagenesisi94R → A: Reduced vacuolization induced by overexpression. 1 Publication1

Keywords - Diseasei

Disease mutation, Osteopetrosis

Organism-specific databases

DisGeNETi29887.
MalaCardsiSNX10.
MIMi615085. phenotype.
OpenTargetsiENSG00000086300.
Orphaneti667. Autosomal recessive malignant osteopetrosis.
PharmGKBiPA37950.

Polymorphism and mutation databases

BioMutaiSNX10.
DMDMi205371824.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002138541 – 201Sorting nexin-10Add BLAST201

Proteomic databases

EPDiQ9Y5X0.
PaxDbiQ9Y5X0.
PeptideAtlasiQ9Y5X0.
PRIDEiQ9Y5X0.

PTM databases

iPTMnetiQ9Y5X0.
PhosphoSitePlusiQ9Y5X0.

Expressioni

Gene expression databases

BgeeiENSG00000086300.
CleanExiHS_SNX10.
ExpressionAtlasiQ9Y5X0. baseline and differential.
GenevisibleiQ9Y5X0. HS.

Organism-specific databases

HPAiHPA015605.
HPA064782.

Interactioni

Subunit structurei

Interacts with ATP6V1D; may play a role in ciliogenesis.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
ARL6IP1Q150415EBI-10329478,EBI-714543

GO - Molecular functioni

  • ATPase binding Source: UniProtKB

Protein-protein interaction databases

BioGridi118940. 3 interactors.
IntActiQ9Y5X0. 2 interactors.
STRINGi9606.ENSP00000343709.

Structurei

Secondary structure

1201
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi11 – 22Combined sources12
Beta strandi25 – 27Combined sources3
Beta strandi29 – 38Combined sources10
Beta strandi46 – 52Combined sources7
Helixi54 – 67Combined sources14
Helixi80 – 82Combined sources3
Helixi88 – 106Combined sources19
Helixi109 – 112Combined sources4
Helixi115 – 122Combined sources8
Helixi127 – 134Combined sources8
Beta strandi138 – 140Combined sources3
Helixi142 – 153Combined sources12

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4ON3X-ray2.60A/B1-201[»]
4PZGX-ray2.80A/B1-201[»]
ProteinModelPortaliQ9Y5X0.
SMRiQ9Y5X0.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini10 – 127PXPROSITE-ProRule annotationAdd BLAST118

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni8 – 125Required for interaction with ATP6V1D1 PublicationAdd BLAST118

Domaini

The PX domain mediates interaction with membranes enriched in phosphatidylinositol 3-phosphate.

Sequence similaritiesi

Belongs to the sorting nexin family.Curated
Contains 1 PX (phox homology) domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiKOG2527. Eukaryota.
COG5391. LUCA.
GeneTreeiENSGT00650000093174.
HOGENOMiHOG000231108.
HOVERGENiHBG054994.
InParanoidiQ9Y5X0.
KOiK17924.
PhylomeDBiQ9Y5X0.
TreeFamiTF332117.

Family and domain databases

Gene3Di3.30.1520.10. 1 hit.
InterProiIPR001683. Phox.
[Graphical view]
PfamiPF00787. PX. 1 hit.
[Graphical view]
SMARTiSM00312. PX. 1 hit.
[Graphical view]
SUPFAMiSSF64268. SSF64268. 1 hit.
PROSITEiPS50195. PX. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9Y5X0-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MFPEQQKEEF VSVWVRDPRI QKEDFWHSYI DYEICIHTNS MCFTMKTSCV
60 70 80 90 100
RRRYREFVWL RQRLQSNALL VQLPELPSKN LFFNMNNRQH VDQRRQGLED
110 120 130 140 150
FLRKVLQNAL LLSDSSLHLF LQSHLNSEDI EACVSGQTKY SVEEAIHKFA
160 170 180 190 200
LMNRRFPEED EEGKKENDID YDSESSSSGL GHSSDDSSSH GCKVNTAPQE

S
Length:201
Mass (Da):23,598
Last modified:September 2, 2008 - v2
Checksum:i665B80734D5E5C72
GO
Isoform 2 (identifier: Q9Y5X0-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-84: Missing.

Note: No experimental confirmation available.
Show »
Length:117
Mass (Da):13,181
Checksum:i1AE71FD546A428CA
GO

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_06929916R → L in OPTB8. 1 PublicationCorresponds to variant rs779298714dbSNPEnsembl.1
Natural variantiVAR_06930032Y → S in OPTB8. 1 PublicationCorresponds to variant rs771038257dbSNPEnsembl.1
Natural variantiVAR_06930151R → P in OPTB8. 1 Publication1
Natural variantiVAR_06930251R → Q in OPTB8; increased expression, produces extensive cytoplasmic vacuolation and impairs bone resorptive function. 1 PublicationCorresponds to variant rs398123011dbSNPEnsembl.1
Natural variantiVAR_046098187S → I.1 PublicationCorresponds to variant rs1053042dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0459201 – 84Missing in isoform 2. 1 PublicationAdd BLAST84

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF121860 mRNA. Translation: AAD27833.1.
AK309162 mRNA. No translation available.
AK312850 mRNA. Translation: BAG35703.1.
AC004540 Genomic DNA. No translation available.
AC010677 Genomic DNA. No translation available.
AC074295 Genomic DNA. No translation available.
CH236948 Genomic DNA. Translation: EAL24234.1.
CH471073 Genomic DNA. Translation: EAW93849.1.
BC034992 mRNA. Translation: AAH34992.1.
CCDSiCCDS5399.1. [Q9Y5X0-1]
CCDS56470.1. [Q9Y5X0-2]
RefSeqiNP_001186764.1. NM_001199835.1. [Q9Y5X0-1]
NP_001186766.1. NM_001199837.1.
NP_001186767.1. NM_001199838.1. [Q9Y5X0-2]
NP_001305127.1. NM_001318198.1.
NP_001305128.1. NM_001318199.1. [Q9Y5X0-1]
NP_037454.2. NM_013322.2. [Q9Y5X0-1]
XP_006715775.1. XM_006715712.2. [Q9Y5X0-1]
UniGeneiHs.741316.

Genome annotation databases

EnsembliENST00000338523; ENSP00000343709; ENSG00000086300. [Q9Y5X0-1]
ENST00000396376; ENSP00000379661; ENSG00000086300. [Q9Y5X0-1]
ENST00000409838; ENSP00000386540; ENSG00000086300. [Q9Y5X0-2]
ENST00000446848; ENSP00000395474; ENSG00000086300. [Q9Y5X0-1]
GeneIDi29887.
KEGGihsa:29887.
UCSCiuc003sxx.4. human. [Q9Y5X0-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF121860 mRNA. Translation: AAD27833.1.
AK309162 mRNA. No translation available.
AK312850 mRNA. Translation: BAG35703.1.
AC004540 Genomic DNA. No translation available.
AC010677 Genomic DNA. No translation available.
AC074295 Genomic DNA. No translation available.
CH236948 Genomic DNA. Translation: EAL24234.1.
CH471073 Genomic DNA. Translation: EAW93849.1.
BC034992 mRNA. Translation: AAH34992.1.
CCDSiCCDS5399.1. [Q9Y5X0-1]
CCDS56470.1. [Q9Y5X0-2]
RefSeqiNP_001186764.1. NM_001199835.1. [Q9Y5X0-1]
NP_001186766.1. NM_001199837.1.
NP_001186767.1. NM_001199838.1. [Q9Y5X0-2]
NP_001305127.1. NM_001318198.1.
NP_001305128.1. NM_001318199.1. [Q9Y5X0-1]
NP_037454.2. NM_013322.2. [Q9Y5X0-1]
XP_006715775.1. XM_006715712.2. [Q9Y5X0-1]
UniGeneiHs.741316.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4ON3X-ray2.60A/B1-201[»]
4PZGX-ray2.80A/B1-201[»]
ProteinModelPortaliQ9Y5X0.
SMRiQ9Y5X0.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi118940. 3 interactors.
IntActiQ9Y5X0. 2 interactors.
STRINGi9606.ENSP00000343709.

PTM databases

iPTMnetiQ9Y5X0.
PhosphoSitePlusiQ9Y5X0.

Polymorphism and mutation databases

BioMutaiSNX10.
DMDMi205371824.

Proteomic databases

EPDiQ9Y5X0.
PaxDbiQ9Y5X0.
PeptideAtlasiQ9Y5X0.
PRIDEiQ9Y5X0.

Protocols and materials databases

DNASUi29887.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000338523; ENSP00000343709; ENSG00000086300. [Q9Y5X0-1]
ENST00000396376; ENSP00000379661; ENSG00000086300. [Q9Y5X0-1]
ENST00000409838; ENSP00000386540; ENSG00000086300. [Q9Y5X0-2]
ENST00000446848; ENSP00000395474; ENSG00000086300. [Q9Y5X0-1]
GeneIDi29887.
KEGGihsa:29887.
UCSCiuc003sxx.4. human. [Q9Y5X0-1]

Organism-specific databases

CTDi29887.
DisGeNETi29887.
GeneCardsiSNX10.
HGNCiHGNC:14974. SNX10.
HPAiHPA015605.
HPA064782.
MalaCardsiSNX10.
MIMi614780. gene.
615085. phenotype.
neXtProtiNX_Q9Y5X0.
OpenTargetsiENSG00000086300.
Orphaneti667. Autosomal recessive malignant osteopetrosis.
PharmGKBiPA37950.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2527. Eukaryota.
COG5391. LUCA.
GeneTreeiENSGT00650000093174.
HOGENOMiHOG000231108.
HOVERGENiHBG054994.
InParanoidiQ9Y5X0.
KOiK17924.
PhylomeDBiQ9Y5X0.
TreeFamiTF332117.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000086300-MONOMER.

Miscellaneous databases

ChiTaRSiSNX10. human.
GenomeRNAii29887.
PROiQ9Y5X0.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000086300.
CleanExiHS_SNX10.
ExpressionAtlasiQ9Y5X0. baseline and differential.
GenevisibleiQ9Y5X0. HS.

Family and domain databases

Gene3Di3.30.1520.10. 1 hit.
InterProiIPR001683. Phox.
[Graphical view]
PfamiPF00787. PX. 1 hit.
[Graphical view]
SMARTiSM00312. PX. 1 hit.
[Graphical view]
SUPFAMiSSF64268. SSF64268. 1 hit.
PROSITEiPS50195. PX. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiSNX10_HUMAN
AccessioniPrimary (citable) accession number: Q9Y5X0
Secondary accession number(s): E9PFH5, Q8IYT5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 1, 2000
Last sequence update: September 2, 2008
Last modified: November 30, 2016
This is version 131 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 7
    Human chromosome 7: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.