SNX1 sorting nexin 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SNX1provided by HGNC
Official Full Name: sorting nexin 1provided by HGNC
Primary source: HGNC:HGNC:11172
See related: Ensembl:ENSG00000028528 MIM:601272; AllianceGenome:HGNC:11172
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: VPS5; HsT17379
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 endosomal protein regulates the cell-surface expression of epidermal growth factor receptor. This protein also has a role in sorting protease-activated receptor-1 from early endosomes to lysosomes. This protein may form oligomeric complexes with family members. This gene results in three transcript variants encoding distinct isoforms. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in thyroid (RPKM 29.5), fat (RPKM 17.2) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 15q22.31

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	15	NC_000015.10 (64095982..64144231)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	15	NC_060939.1 (61903135..61951407)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	15	NC_000015.9 (64388181..64436430)

Chromosome 15 - NC_000015.10 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
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?

Biochemical basis for an interaction between SNX27 and the flexible SNX1 N-terminus.
Title: Biochemical basis for an interaction between SNX27 and the flexible SNX1 N-terminus.
Sorting nexin 1 loss results in increased oxidative stress and hypertension.
Title: Sorting nexin 1 loss results in increased oxidative stress and hypertension.
Data suggest that GLP1R signaling in pancreatic beta-cells leading to insulin secretion involves interactions of GLP1R with HIP1, SNX1, and SNX27; HIP1 appears to regulate coupling of cell surface GLP1R activation with endocytosis; SNX1 and SNX27 appear to control balance between GLP1R plasma membrane recycling and lysosomal degradation.
Title: A Targeted RNAi Screen Identifies Endocytic Trafficking Factors That Control GLP-1 Receptor Signaling in Pancreatic β-Cells.
SNX1 was down-regulated in CRC and associated with poor prognosis. Our data also showed that SNX1 inhibited the proliferation of CRC cells and increased the sensitivity to the most commonly used drugs for CRC.
Title: Down-regulation of SNX1 predicts poor prognosis and contributes to drug resistance in colorectal cancer.
miR-95 functions as an oncogene role in non-small cell lung cancer cells by directly targeting SNX1.
Title: MiR-95 induces proliferation and chemo- or radioresistance through directly targeting sorting nexin1 (SNX1) in non-small cell lung cancer.
Results show that suppression of EGFR membrane recycling by SNX1 appears to be critical for the activation of EGFR /PI3K/AKT signaling pathway in human lung cancer cells.
Title: EGF‑stimulated AKT activation is mediated by EGFR recycling via an early endocytic pathway in a gefitinib‑resistant human lung cancer cell line.
we suggest that SNX1 is involved in the negative regulation of ligand-induced EGFR phosphorylation and mediates EGFR/pEGFR trafficking out of early endosomes
Title: Silencing of SNX1 by siRNA stimulates the ligand-induced endocytosis of EGFR and increases EGFR phosphorylation in gefitinib-resistant human lung cancer cell lines.
SNX1 has a crucial role in D(5)R trafficking and SNX1 depletion results in D(5)R dysfunction and thus may represent a novel mechanism for the pathogenesis of essential hypertension
Title: Sorting nexin 1 loss results in D5 dopamine receptor dysfunction in human renal proximal tubule cells and hypertension in mice.
This study found that significant evidence of association with SNX1 (VEGAS p = 0.035) in patient with Alzheimer disease.
Title: Identification of Alzheimer disease-associated variants in genes that regulate retromer function.
SNX4, but not SNX1 and SNX8, is associated with the Rab11-recycling endosomes and that a high frequency of SNX4-mediated tubule formation is observed as endosomes undergo Rab4-to-Rab11 transition.
Title: SNX-BAR-mediated endosome tubulation is co-ordinated with endosome maturation.

Submit: New GeneRIF Correction See all GeneRIFs (25)

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH47502 (e-PCR)
- UniSTS:65543

SHGC-24058 (e-PCR)
- UniSTS:65544

D15S1176 (e-PCR)
- UniSTS:59434

SHGC-132367 (e-PCR)
- UniSTS:170797

REN94580 (e-PCR)
- UniSTS:419378

STS-H15134 (e-PCR)
- UniSTS:41047

Bdaa7f10 (e-PCR)
- UniSTS:65690

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables cadherin binding	HDA more info	PubMed
enables epidermal growth factor receptor binding	IDA Inferred from Direct Assay more info	PubMed
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables insulin receptor binding	IDA Inferred from Direct Assay more info	PubMed
enables leptin receptor binding	IDA Inferred from Direct Assay more info	PubMed
enables phosphatidylinositol binding	IBA Inferred from Biological aspect of Ancestor more info
enables phosphatidylinositol binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein heterodimerization activity	IPI Inferred from Physical Interaction more info	PubMed
enables protein homodimerization activity	IPI Inferred from Physical Interaction more info	PubMed
enables transferrin receptor binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in early endosome to Golgi transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in early endosome to Golgi transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in intracellular protein transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in lamellipodium morphogenesis	IDA Inferred from Direct Assay more info	PubMed
involved_in receptor internalization	IMP Inferred from Mutant Phenotype more info	PubMed
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 Golgi apparatus	IEA Inferred from Electronic Annotation more info
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
is_active_in endosome membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in endosome membrane	IDA Inferred from Direct Assay more info	PubMed
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info
located_in lamellipodium	IEA Inferred from Electronic Annotation more info
located_in lysosome	IDA Inferred from Direct Assay more info
located_in membrane	IDA Inferred from Direct Assay more info	PubMed
part_of protein-containing complex	IDA Inferred from Direct Assay more info	PubMed
part_of retromer complex	IDA Inferred from Direct Assay more info	PubMed
part_of retromer, tubulation complex	IPI Inferred from Physical Interaction more info	PubMed
part_of retromer, tubulation complex	NAS Non-traceable Author Statement more info	PubMed
located_in vesicle	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: sorting nexin-1

Names: sorting nexin 1A

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_029708.1 RefSeqGene

Range

5099..53348

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001242933.2 → NP_001229862.1 sorting nexin-1 isoform d

Status: REVIEWED

Description

Transcript Variant: This variant (4) uses an alternate splice site that causes a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (d) has a distinct and longer C-terminus, compared to isoform a.

Source sequence(s)

AC100840, AK128179, BX108623, DB455188

Consensus CDS

CCDS58371.1

UniProtKB/TrEMBL

Q53GY8

Related

ENSP00000261889.5, ENST00000261889.9

Conserved Domains (3) summary

cd07281
Location:145 → 268

PX_SNX1; The phosphoinositide binding Phox Homology domain of Sorting Nexin 1

pfam03700
Location:55 → 130

Sorting_nexin; Sorting nexin, N-terminal domain

cl12013
Location:286 → 506

BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature
NM_003099.5 → NP_003090.2 sorting nexin-1 isoform a

See identical proteins and their annotated locations for NP_003090.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes isoform a.

Source sequence(s)

AC100840, AK291752, BX108623, DB455188

Consensus CDS

CCDS32266.1

UniProtKB/Swiss-Prot

A6NM19, A8K6T7, H0Y2M5, O60750, O60751, Q13596, Q6ZRJ8

UniProtKB/TrEMBL

Q53GY8

Related

ENSP00000453785.1, ENST00000559844.6

Conserved Domains (3) summary

cd07281
Location:145 → 268

PX_SNX1; The phosphoinositide binding Phox Homology domain of Sorting Nexin 1

cd07665
Location:286 → 519

BAR_SNX1; The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 1

pfam03700
Location:11 → 90

Sorting_nexin; Sorting nexin, N-terminal domain
NM_148955.4 → NP_683758.1 sorting nexin-1 isoform b

See identical proteins and their annotated locations for NP_683758.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an in-frame segment of the 5' coding region, compared to variant 1. It encodes a shorter isoform (b), also known as SNX1A, that is missing an internal segment compared to isoform a.

Source sequence(s)

AC100840, AF065484, BX108623, DB455188

Consensus CDS

CCDS32268.1

UniProtKB/TrEMBL

Q53GY8

Related

ENSP00000453567.1, ENST00000561026.5

Conserved Domains (2) summary

cd07665
Location:221 → 454

BAR_SNX1; The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 1

cl02563
Location:91 → 203

PX_domain; The Phox Homology domain, a phosphoinositide binding module

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

NC_000015.10 Reference GRCh38.p14 Primary Assembly

Range

64095982..64144231

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GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

NC_060939.1 Alternate T2T-CHM13v2.0

Range

61903135..61951407

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GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_152826.2: Suppressed sequence

Description

NM_152826.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.