SNX10 sorting nexin 10 [Homo sapiens (human)] - Gene

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: mouse all
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Genomic context

Location:: 7p15.2

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2023_03	current	GRCh38.p14 (GCF_000001405.40)	7	NC_000007.14 (26291862..26374383)
RS_2023_03	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_000007.14 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Overexpression Pattern of miR-301b in Osteosarcoma and Its Relevance with Osteosarcoma Cellular Behaviors via Modulating SNX10.
Title: Overexpression Pattern of miR-301b in Osteosarcoma and Its Relevance with Osteosarcoma Cellular Behaviors via Modulating SNX10.
Osteopetrosis associated with PLEKHM1 and SNX10 genes, both involved in osteoclast vesicular trafficking.
Title: Osteopetrosis associated with PLEKHM1 and SNX10 genes, both involved in osteoclast vesicular trafficking.
Identification of Key Amino Acid Residues Involved in the Localization of Sorting Nexin 10 and Induction of Vacuole Formation.
Title: Identification of Key Amino Acid Residues Involved in the Localization of Sorting Nexin 10 and Induction of Vacuole Formation.
SNX10-mediated LPS sensing causes intestinal barrier dysfunction via a caspase-5-dependent signaling cascade.
Title: SNX10-mediated LPS sensing causes intestinal barrier dysfunction via a caspase-5-dependent signaling cascade.
SNX10 and PTGDS are associated with the progression and prognosis of cervical squamous cell carcinoma.
Title: SNX10 and PTGDS are associated with the progression and prognosis of cervical squamous cell carcinoma.
SNX10 (sorting nexin 10) inhibits colorectal cancer initiation and progression by controlling autophagic degradation of SRC.
Title: SNX10 (sorting nexin 10) inhibits colorectal cancer initiation and progression by controlling autophagic degradation of SRC.
Sorting Nexin 10 Mediates Metabolic Reprogramming of Macrophages in Atherosclerosis Through the Lyn-Dependent TFEB Signaling Pathway.
Title: Sorting Nexin 10 Mediates Metabolic Reprogramming of Macrophages in Atherosclerosis Through the Lyn-Dependent TFEB Signaling Pathway.
Does Decreased SNX10 Serve as a Novel Risk Factor in Atrial Fibrillation of the Valvular Heart Disease? - A Case-Control Study.
Title: Does Decreased SNX10 Serve as a Novel Risk Factor in Atrial Fibrillation of the Valvular Heart Disease? - A Case-Control Study.
SNX10 gene mutation in infantile malignant osteopetrosis: A case report and literature review.", trans "SNX101.
Title: SNX10 gene mutation in infantile malignant osteopetrosis: A case report and literature review.
this work revealed that SNX10 controls mTOR activation through regulating chaperone-mediated autophagy-dependent amino-acid metabolism.
Title: Sorting nexin 10 controls mTOR activation through regulating amino-acid metabolism in colorectal cancer.

Submit: New GeneRIF Correction See all GeneRIFs (22)

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

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 EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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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

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

WI-21086 (e-PCR)
- UniSTS:35351

SHGC-55990 (e-PCR)
- UniSTS:82792

A003A21 (e-PCR)
- UniSTS:36573

SHGC-143124 (e-PCR)
- UniSTS:174065

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	PubMed
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	PubMed
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	PubMed

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	PubMed
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

General protein information

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Preferred Names: sorting nexin-10

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.

Genomic

NG_033902.1 RefSeqGene

Range

4968..87489

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001199835.1 → NP_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

Q8IYT5, Q9Y5X0

UniProtKB/TrEMBL

A0A024RA70, B4DJM0

Related

ENSP00000395474.3, ENST00000446848.6

Conserved Domains (1) summary

cd06898
Location:12 → 109

PX_SNX10; The phosphoinositide binding Phox Homology domain of Sorting Nexin 10
NM_001199837.3 → NP_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/Swiss-Prot

Q9Y5X0

UniProtKB/TrEMBL

B4DJM0

Related

ENST00000698092.1

Conserved Domains (1) summary

cd06898
Location:9 → 106

PX_SNX10; The phosphoinositide binding Phox Homology domain of Sorting Nexin 10
NM_001199838.2 → NP_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:1 → 40

PX_domain; The Phox Homology domain, a phosphoinositide binding module
NM_001318198.1 → NP_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

Conserved Domains (1) summary

cd06898
Location:38 → 135

PX_SNX10; The phosphoinositide binding Phox Homology domain of Sorting Nexin 10
NM_001318199.3 → NP_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

Q8IYT5, Q9Y5X0

UniProtKB/TrEMBL

A0A024RA70, Q8N5Z3

Related

ENSP00000379661.1, ENST00000396376.5

Conserved Domains (1) summary

cd06898
Location:12 → 109

PX_SNX10; The phosphoinositide binding Phox Homology domain of Sorting Nexin 10
NM_001362753.1 → NP_001349682.1 sorting nexin-10 isoform 4

Status: REVIEWED

Source sequence(s)

AK316088, BC034992, BM147840, BX648363, DB479030

UniProtKB/TrEMBL

B4DJM0

Conserved Domains (1) summary

cd06898
Location:38 → 135

PX_SNX10; The phosphoinositide binding Phox Homology domain of Sorting Nexin 10
NM_001362754.1 → NP_001349683.1 sorting nexin-10 isoform 4

Status: REVIEWED

Source sequence(s)

AK312850, AK316088, BC034992, BM147840, BX648363

UniProtKB/TrEMBL

B4DJM0

Conserved Domains (1) summary

cd06898
Location:38 → 135

PX_SNX10; The phosphoinositide binding Phox Homology domain of Sorting Nexin 10
NM_013322.3 → NP_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

Q8IYT5, Q9Y5X0

UniProtKB/TrEMBL

A0A024RA70, Q8N5Z3

Related

ENSP00000343709.5, ENST00000338523.9

Conserved Domains (1) summary

cd06898
Location:12 → 109

PX_SNX10; The phosphoinositide binding Phox Homology domain of Sorting Nexin 10

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_03

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000007.14 Reference GRCh38.p14 Primary Assembly

Range

26291862..26374383

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

See identical proteins and their annotated locations for XP_006715775.1

UniProtKB/Swiss-Prot

Q8IYT5, Q9Y5X0

UniProtKB/TrEMBL

A0A024RA70

Related

ENST00000698091.1

Conserved Domains (1) summary

cd06898
Location:12 → 109

PX_SNX10; The phosphoinositide binding Phox Homology domain of Sorting Nexin 10
XM_047420282.1 → XP_047276238.1 sorting nexin-10 isoform X1

UniProtKB/TrEMBL

B4DJM0
XM_047420283.1 → XP_047276239.1 sorting nexin-10 isoform X3

UniProtKB/TrEMBL

C9JQ16

Related

ENSP00000387274.1, ENST00000409367.6

Alternate T2T-CHM13v2.0

Genomic

NC_060931.1 Alternate T2T-CHM13v2.0

Range

26427536..26510069

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/Swiss-Prot

Q8IYT5

UniProtKB/TrEMBL

A0A024RA70
XM_054358025.1 → XP_054214000.1 sorting nexin-10 isoform X1

UniProtKB/TrEMBL

B4DJM0
XM_054358027.1 → XP_054214002.1 sorting nexin-10 isoform X3

UniProtKB/TrEMBL

C9JQ16