SNX6 sorting nexin 6 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SNX6provided by HGNC
Official Full Name: sorting nexin 6provided by HGNC
Primary source: HGNC:HGNC:14970
See related: Ensembl:ENSG00000129515 MIM:606098; AllianceGenome:HGNC:14970
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: TFAF2; MSTP010
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 associates with the long isoform of the leptin receptor, the transforming growth factor-beta family of receptor serine-threonine kinases, and with receptor tyrosine kinases for platelet-derived growth factor, insulin, and epidermal growth factor. This protein may form oligomeric complexes with family member proteins through interactions of both the PX domain and the coiled coil regions of the molecules. Translocation of this protein from the cytoplasm to the nucleus occurs after binding to proviral integration site 1 protein. This gene results in two transcripts encoding two distinct isoforms. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in placenta (RPKM 36.9), duodenum (RPKM 33.6) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 14q13.1

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	14	NC_000014.9 (34561093..34630148, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	14	NC_060938.1 (28757116..28826173, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	14	NC_000014.8 (35030299..35099354, complement)

Chromosome 14 - NC_000014.9 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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?

Sorting nexin 6 interacts with Cullin3 and regulates programmed death ligand 1 expression.
Title: Sorting nexin 6 interacts with Cullin3 and regulates programmed death ligand 1 expression.
The studies identify a sorting motif and provide molecular insight into an evolutionary conserved coat complex, the 'Endosomal SNX-BAR sorting complex for promoting exit 1' (ESCPE-1), which couples sorting motif recognition to the BAR-domain-mediated biogenesis of cargo-enriched tubulo-vesicular transport carriers.
Title: Molecular identification of a BAR domain-containing coat complex for endosomal recycling of transmembrane proteins.
The data imply that Rab32 is linked to SNX6/retromer trafficking at the Golgi, and also suggests a possible connection between the retromer and Rab32 in the trafficking and biological functions of LRRK2.
Title: Rab32 interacts with SNX6 and affects retromer-dependent Golgi trafficking.
Data indicate that sorting nexin 6 (SNX6) serves as a biomarker for predicting prognosis of pancreatic cancer.
Title: SNX6 predicts poor prognosis and contributes to the metastasis of pancreatic cancer cells via activating epithelial-mesenchymal transition.
study confirms the utility of proximity-labeling methods, such as BioID, to screen for interactors of cell-surface receptors and has uncovered a role of one of these interactors, SNX6, in the IGF1R signaling cascade.
Title: The proximity-labeling technique BioID identifies sorting nexin 6 as a member of the insulin-like growth factor 1 (IGF1)-IGF1 receptor pathway.
These results identify SNX6 as a key regulator of lamin A synthesis and incorporation into the nuclear envelope.
Title: Sorting nexin 6 enhances lamin a synthesis and incorporation into the nuclear envelope.
Study observed that SNX6 increases BRMS1-dependent transcriptional repression. Moreover, over-expression of SNX6 was capable of diminishing trans-activation in a dose-dependent manner.
Title: Sorting nexin 6 interacts with breast cancer metastasis suppressor-1 and promotes transcriptional repression.
SNX6 modulates the retrograde trafficking and basal levels of BACE1, thereby regulating BACE1-mediated APP processing and Abeta biogenesis
Title: Proteomic identification of sorting nexin 6 as a negative regulator of BACE1-mediated APP processing.
These observations indicate that in addition to SNX1/2, SNX6 in association with the dynein/dynactin complex drives the formation and movement of tubular retrograde intermediates.
Title: The retromer component SNX6 interacts with dynactin p150(Glued) and mediates endosome-to-TGN transport.
SNX5 and SNX6 may constitute functional equivalents of Vps17p in mammalian retromer
Title: A loss-of-function screen reveals SNX5 and SNX6 as potential components of the mammalian retromer.

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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

EBI GWAS Catalog

Description
A possible mechanism behind autoimmune disorders discovered by genome-wide linkage and association analysis in celiac disease. 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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Protein interactions

Protein	Gene	Interaction	Pubs
Nef	nef	Genome-wide shRNA screening identifies SNX6, which is required for HIV-1 Nef-induced downregulation of CD4 in HeLa CD4+ cells	PubMed

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D14S827 (e-PCR)
- UniSTS:29193

G35892 (e-PCR)
- UniSTS:51474

MARC_4171-4172:996679463:3 (e-PCR)
- UniSTS:269340

D14S665E (e-PCR)
- UniSTS:22609

RH44760 (e-PCR)
- UniSTS:25754

LOC510454 (e-PCR)
- UniSTS:519069

G35904 (e-PCR)
- UniSTS:52135

G35755 (e-PCR)
- UniSTS:57774

RH81064 (e-PCR)
- UniSTS:91072

D14S1170 (e-PCR)
- UniSTS:12003

G36182 (e-PCR)
- UniSTS:75499

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables dynactin binding	IBA Inferred from Biological aspect of Ancestor more info
enables dynactin binding	IDA Inferred from Direct Assay more info	PubMed
enables phosphatidylinositol binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein homodimerization activity	IPI Inferred from Physical Interaction more info	PubMed
enables type I transforming growth factor beta receptor binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in cellular response to amyloid-beta	IGI Inferred from Genetic Interaction more info	PubMed
involved_in cellular response to epidermal growth factor stimulus	IEA Inferred from Electronic Annotation more info
involved_in intracellular protein transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in intracellular protein transport	NAS Non-traceable Author Statement more info	PubMed
involved_in negative regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of epidermal growth factor-activated receptor activity	NAS Non-traceable Author Statement more info	PubMed
involved_in negative regulation of neuron apoptotic process	IGI Inferred from Genetic Interaction more info	PubMed
involved_in negative regulation of transforming growth factor beta receptor signaling pathway	IDA Inferred from Direct Assay more info	PubMed
NOT involved_in regulation of histamine secretion by mast cell	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of macroautophagy	NAS Non-traceable Author Statement more info	PubMed
involved_in regulation of postsynaptic membrane neurotransmitter receptor levels	IEA Inferred from Electronic Annotation more info
involved_in retrograde transport, endosome to Golgi	IBA Inferred from Biological aspect of Ancestor more info
involved_in retrograde transport, endosome to Golgi	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in retrograde transport, endosome to Golgi	NAS Non-traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in early endosome membrane	IDA Inferred from Direct Assay more info	PubMed
is_active_in endosome	IBA Inferred from Biological aspect of Ancestor more info
located_in endosome	IDA Inferred from Direct Assay more info
located_in glutamatergic synapse	IEA Inferred from Electronic Annotation more info
located_in lysosome	IDA Inferred from Direct Assay more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in postsynaptic early endosome	IEA Inferred from Electronic Annotation more info
part_of retromer complex	IDA Inferred from Direct Assay more info	PubMed
part_of retromer, tubulation complex	NAS Non-traceable Author Statement more info	PubMed
located_in tubular endosome	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: sorting nexin-6

Names: TRAF4-associated factor 2; tumor necrosis factor receptor-associated factor 4(TRAF4)-associated factor 2

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)

NM_001366519.1 → NP_001353448.1 sorting nexin-6 isoform c

Status: REVIEWED

Source sequence(s)

AL445363, AL445883

UniProtKB/TrEMBL

A8K885

Conserved Domains (2) summary

cl02563
Location:30 → 133

PX_domain; The Phox Homology domain, a phosphoinositide binding module

cl12013
Location:149 → 366

BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature
NM_021249.5 → NP_067072.3 sorting nexin-6 isoform a

See identical proteins and their annotated locations for NP_067072.3

Status: REVIEWED

Description

Transcript Variant: This variant (1) retains an intron in the 5' UTR and represents the longest transcript. The resulting isoform (a) has a shorter N-terminus compared to isoform b.

Source sequence(s)

AF121856, AI446034, AK124315, AL445883, BC001798, BI870378, DB021488

Consensus CDS

CCDS9648.1

UniProtKB/TrEMBL

B4DJS7

Related

ENSP00000379779.3, ENST00000396526.7

Conserved Domains (2) summary

cl02563
Location:1 → 54

PX_domain; The Phox Homology domain, a phosphoinositide binding module

cl12013
Location:70 → 287

BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature
NM_152233.4 → NP_689419.3 sorting nexin-6 isoform b

Status: REVIEWED

Description

Transcript Variant: This variant (2) encodes the longest isoform (b).

Source sequence(s)

AF121856, AI446034, AK124315, BI870378, DB021488, U83194

Consensus CDS

CCDS41942.2

UniProtKB/Swiss-Prot

C0H5W9, Q9UNH7, Q9Y449

UniProtKB/TrEMBL

A8K885

Related

ENSP00000355217.5, ENST00000362031.10

Conserved Domains (2) summary

cd07292
Location:30 → 170

PX_SNX6; The phosphoinositide binding Phox Homology domain of Sorting Nexin 6

cd07662
Location:186 → 403

BAR_SNX6; The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 6

RNA

NR_159357.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AL445363, AL445883
NR_159358.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AL445363, AL445883