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SNX1 sorting nexin 1 [ Homo sapiens (human) ]

Gene ID: 6642, updated on 10-Dec-2024

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
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Genomic context

See SNX1 in Genome Data Viewer
Location:
15q22.31
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (64095982..64144231)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (61903135..61951407)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (64388181..64436430)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101928988 Neighboring gene death associated protein kinase 2 Neighboring gene Sharpr-MPRA regulatory region 12240 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:64264631-64265378 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:64277639-64278140 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:64290279-64290780 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6524 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9547 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9548 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:64318331-64318496 Neighboring gene NANOG hESC enhancer GRCh37_chr15:64330918-64331419 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9549 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9550 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6525 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6526 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6527 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:64342658-64343204 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9551 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9552 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:64385112-64385674 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9554 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9556 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9555 Neighboring gene Sharpr-MPRA regulatory region 7733 Neighboring gene cytosolic iron-sulfur assembly component 2A Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9557 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9558 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9559 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:64437862-64438378 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9560 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6528 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6529 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:64445879-64446610 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9561 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:64453780-64454344 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:64454578-64455078 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:64455079-64455579 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9565 Neighboring gene sorting nexin 22 Neighboring gene casein kinase 1 gamma 1 Neighboring gene peptidylprolyl isomerase B Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:64538178-64538678 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:64538679-64539179 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9566 Neighboring gene Sharpr-MPRA regulatory region 12494 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:64618290-64619150 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:64619151-64620010 Neighboring gene small nucleolar RNA SNORA48

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 Functions

What's a GeneRIF?

Pathways from PubChem

Interactions

General gene information

Clone Names

  • MGC8664

Gene Ontology Provided by GOA

Component Evidence Code Pubs
located_in Golgi apparatus  
located_in cytoplasm PubMed 
located_in cytosol  
located_in early endosome membrane PubMed 
is_active_in endosome  
located_in endosome  
is_active_in endosome membrane  
located_in endosome membrane PubMed 
located_in intracellular membrane-bounded organelle  
located_in lamellipodium  
located_in lysosome  
located_in membrane PubMed 
part_of protein-containing complex PubMed 
part_of retromer complex PubMed 
part_of retromer, tubulation complex PubMed 
part_of retromer, tubulation complex PubMed 
located_in vesicle PubMed 

General protein information

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

  1. NG_029708.1 RefSeqGene

    Range
    5099..53348
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001242933.2NP_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:145268
    PX_SNX1; The phosphoinositide binding Phox Homology domain of Sorting Nexin 1
    pfam03700
    Location:55130
    Sorting_nexin; Sorting nexin, N-terminal domain
    cl12013
    Location:286506
    BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature
  2. NM_003099.5NP_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:145268
    PX_SNX1; The phosphoinositide binding Phox Homology domain of Sorting Nexin 1
    cd07665
    Location:286519
    BAR_SNX1; The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 1
    pfam03700
    Location:1190
    Sorting_nexin; Sorting nexin, N-terminal domain
  3. NM_148955.4NP_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:221454
    BAR_SNX1; The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 1
    cl02563
    Location:91203
    PX_domain; The Phox Homology domain, a phosphoinositide binding module

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    64095982..64144231
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    61903135..61951407
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

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