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SORT1 sortilin 1 [ Homo sapiens (human) ]

Gene ID: 6272, updated on 6-Jan-2019

Summary

Official Symbol
SORT1provided by HGNC
Official Full Name
sortilin 1provided by HGNC
Primary source
HGNC:HGNC:11186
See related
Ensembl:ENSG00000134243 MIM:602458
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
NT3; Gp95; NTR3; LDLCQ6
Summary
This gene encodes a member of the VPS10-related sortilin family of proteins. The encoded preproprotein is proteolytically processed by furin to generate the mature receptor. This receptor plays a role in the trafficking of different proteins to either the cell surface, or subcellular compartments such as lysosomes and endosomes. Expression levels of this gene may influence the risk of myocardial infarction in human patients. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2015]
Expression
Broad expression in brain (RPKM 47.1), testis (RPKM 30.3) and 22 other tissues See more
Orthologs

Genomic context

See SORT1 in Genome Data Viewer
Location:
1p13.3; 1p21.3-p13.1
Exon count:
23
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 1 NC_000001.11 (109309565..109397945, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (109852187..109940563, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene proline and serine rich coiled-coil 1 Neighboring gene myosin binding protein H like Neighboring gene proteasome subunit alpha 5 Neighboring gene synaptophysin like 2

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 FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Low density lipoprotein cholesterol level quantitative trait locus 6
MedGen: C3150834 OMIM: 613589 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

Description
A genome-wide association study in Europeans and South Asians identifies five new loci for coronary artery disease.
NHGRI GWA Catalog
Biological, clinical and population relevance of 95 loci for blood lipids.
NHGRI GWA Catalog
Common variants at 30 loci contribute to polygenic dyslipidemia.
NHGRI GWA Catalog
Discovery and refinement of loci associated with lipid levels.
NHGRI GWA Catalog
Genome-wide association analysis of metabolic traits in a birth cohort from a founder population.
NHGRI GWA Catalog
Genome-wide association of early-onset myocardial infarction with single nucleotide polymorphisms and copy number variants.
NHGRI GWA Catalog
Genome-wide association of lipid-lowering response to statins in combined study populations.
NHGRI GWA Catalog
Genome-wide association study evaluating lipoprotein-associated phospholipase A2 mass and activity at baseline and after rosuvastatin therapy.
NHGRI GWA Catalog
Genome-wide association study of coronary heart disease and its risk factors in 8,090 African Americans: the NHLBI CARe Project.
NHGRI GWA Catalog
Genome-wide screen identifies rs646776 near sortilin as a regulator of progranulin levels in human plasma.
NHGRI GWA Catalog
Identification of ADAMTS7 as a novel locus for coronary atherosclerosis and association of ABO with myocardial infarction in the presence of coronary atherosclerosis: two genome-wide association studies.
NHGRI GWA Catalog
Large-scale association analysis identifies 13 new susceptibility loci for coronary artery disease.
NHGRI GWA Catalog
Large-scale genome-wide association studies in East Asians identify new genetic loci influencing metabolic traits.
NHGRI GWA Catalog
New loci associated with kidney function and chronic kidney disease.
NHGRI GWA Catalog
Newly identified loci that influence lipid concentrations and risk of coronary artery disease.
NHGRI GWA Catalog
Shared genetic susceptibility to ischemic stroke and coronary artery disease: a genome-wide analysis of common variants.
NHGRI GWA Catalog
Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans.
NHGRI GWA Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp160, precursor env HIV-1 gp160 interacts with SORT1; predicted interaction to be within the endoplasmic reticulum to Golgi transport PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Brain-Derived Neurotrophic Factor (BDNF) signaling pathway, organism-specific biosystem (from WikiPathways)
    Brain-Derived Neurotrophic Factor (BDNF) signaling pathway, organism-specific biosystemBrain-derived neurotrophic factor (BDNF) is a neurotrophin essential for growth, differentiation, plasticity, and survival of neurons. BDNF is also required for processes such as energy metabolism, b...
  • Clathrin derived vesicle budding, organism-specific biosystem (from REACTOME)
    Clathrin derived vesicle budding, organism-specific biosystemThere at least two classes of clathrin coated vesicles in cells, one predominantly Golgi-associated, involved in budding from the trans-Golgi network and the other at the plasma membrane. Here the cl...
  • Golgi Associated Vesicle Biogenesis, organism-specific biosystem (from REACTOME)
    Golgi Associated Vesicle Biogenesis, organism-specific biosystemProteins that have been synthesized, processed and sorted eventually reach the final steps of the secretory pathway. This pathway is responsible not only for proteins that are secreted from the cell ...
  • Lysosome, organism-specific biosystem (from KEGG)
    Lysosome, organism-specific biosystemLysosomes are membrane-delimited organelles in animal cells serving as the cell's main digestive compartment to which all sorts of macromolecules are delivered for degradation. They contain more than...
  • Lysosome, conserved biosystem (from KEGG)
    Lysosome, conserved biosystemLysosomes are membrane-delimited organelles in animal cells serving as the cell's main digestive compartment to which all sorts of macromolecules are delivered for degradation. They contain more than...
  • Membrane Trafficking, organism-specific biosystem (from REACTOME)
    Membrane Trafficking, organism-specific biosystemThe secretory membrane system allows a cell to regulate delivery of newly synthesized proteins, carbohydrates, and lipids to the cell surface, a necessity for growth and homeostasis. The system is ma...
  • Neurotrophin signaling pathway, organism-specific biosystem (from KEGG)
    Neurotrophin signaling pathway, organism-specific biosystemNeurotrophins are a family of trophic factors involved in differentiation and survival of neural cells. The neurotrophin family consists of nerve growth factor (NGF), brain derived neurotrophic facto...
  • Neurotrophin signaling pathway, conserved biosystem (from KEGG)
    Neurotrophin signaling pathway, conserved biosystemNeurotrophins are a family of trophic factors involved in differentiation and survival of neural cells. The neurotrophin family consists of nerve growth factor (NGF), brain derived neurotrophic facto...
  • Vesicle-mediated transport, organism-specific biosystem (from REACTOME)
    Vesicle-mediated transport, organism-specific biosystemThe transit of proteins and other cargo through the cell requires a cellular transport process in which transported substances are moved in membrane-bounded vesicles. Transported substances are enclo...
  • p75(NTR)-mediated signaling, organism-specific biosystem (from Pathway Interaction Database)
    p75(NTR)-mediated signaling, organism-specific biosystem
    p75(NTR)-mediated signaling
  • trans-Golgi Network Vesicle Budding, organism-specific biosystem (from REACTOME)
    trans-Golgi Network Vesicle Budding, organism-specific biosystemAfter passing through the Golgi complex, secretory cargo is packaged into post-Golgi transport intermediates (post-Golgi), which translocate plus-end directed along microtubules to the plasma membran...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enzyme binding IPI
Inferred from Physical Interaction
more info
PubMed 
nerve growth factor binding IPI
Inferred from Physical Interaction
more info
PubMed 
nerve growth factor receptor activity IDA
Inferred from Direct Assay
more info
PubMed 
neurotensin receptor activity, non-G protein-coupled IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
G protein-coupled receptor signaling pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
Golgi to endosome transport IDA
Inferred from Direct Assay
more info
PubMed 
endocytosis IDA
Inferred from Direct Assay
more info
PubMed 
endosome to lysosome transport IDA
Inferred from Direct Assay
more info
PubMed 
endosome transport via multivesicular body sorting pathway IDA
Inferred from Direct Assay
more info
PubMed 
extrinsic apoptotic signaling pathway via death domain receptors IDA
Inferred from Direct Assay
more info
PubMed 
glucose import IMP
Inferred from Mutant Phenotype
more info
PubMed 
multicellular organism development IEA
Inferred from Electronic Annotation
more info
 
myotube differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of fat cell differentiation IEA
Inferred from Electronic Annotation
more info
 
negative regulation of lipoprotein lipase activity IDA
Inferred from Direct Assay
more info
PubMed 
nerve growth factor signaling pathway IEA
Inferred from Electronic Annotation
more info
 
neuropeptide signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
neurotrophin TRK receptor signaling pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
ossification IEA
Inferred from Electronic Annotation
more info
 
plasma membrane to endosome transport IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of epithelial cell apoptotic process IEA
Inferred from Electronic Annotation
more info
 
regulation of gene expression IMP
Inferred from Mutant Phenotype
more info
PubMed 
response to insulin IMP
Inferred from Mutant Phenotype
more info
PubMed 
vesicle organization IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
Golgi apparatus IDA
Inferred from Direct Assay
more info
PubMed 
Golgi cisterna membrane IEA
Inferred from Electronic Annotation
more info
 
cell surface IDA
Inferred from Direct Assay
more info
PubMed 
clathrin-coated pit IDA
Inferred from Direct Assay
more info
PubMed 
clathrin-coated vesicle IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasmic vesicle IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasmic vesicle membrane IEA
Inferred from Electronic Annotation
more info
 
cytosol IDA
Inferred from Direct Assay
more info
 
dendrite IEA
Inferred from Electronic Annotation
more info
 
early endosome IDA
Inferred from Direct Assay
more info
PubMed 
endoplasmic reticulum membrane IEA
Inferred from Electronic Annotation
more info
 
endosome membrane IEA
Inferred from Electronic Annotation
more info
 
integral component of membrane IDA
Inferred from Direct Assay
more info
PubMed 
lysosomal membrane IEA
Inferred from Electronic Annotation
more info
 
neuronal cell body IEA
Inferred from Electronic Annotation
more info
 
nuclear membrane IEA
Inferred from Electronic Annotation
more info
 
perinuclear region of cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
plasma membrane NAS
Non-traceable Author Statement
more info
PubMed 
trans-Golgi network transport vesicle IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
sortilin
Names
100 kDa NT receptor
glycoprotein 95
neurotensin receptor 3

NCBI Reference Sequences (RefSeq)

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_028280.1 RefSeqGene

    Range
    4997..93377
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001205228.1NP_001192157.1  sortilin isoform 2

    See identical proteins and their annotated locations for NP_001192157.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence and uses an alternate in-frame splice junction at the 5' end of an exon compared to variant 1.The resulting isoform (2) is shorter at the N-terminus and lacks an internal aa compared to isoform 1.
    Source sequence(s)
    AA782785, AK301548, AL390252, BC023542, DA023768, DB045034
    Consensus CDS
    CCDS55618.1
    UniProtKB/Swiss-Prot
    Q99523
    Related
    ENSP00000438597.1, ENST00000538502.5
    Conserved Domains (2) summary
    smart00602
    Location:1604
    VPS10; VPS10 domain
    pfam15901
    Location:437604
    Sortilin_C; Sortilin, neurotensin receptor 3, C-terminal
  2. NM_002959.7NP_002950.3  sortilin isoform 1 preproprotein

    See identical proteins and their annotated locations for NP_002950.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AL390252, BC023542, DA023768, DB045034
    Consensus CDS
    CCDS798.1
    UniProtKB/Swiss-Prot
    Q99523
    Related
    ENSP00000256637.6, ENST00000256637.7
    Conserved Domains (2) summary
    smart00602
    Location:133741
    VPS10; VPS10 domain
    pfam15901
    Location:574741
    Sortilin_C; Sortilin, neurotensin receptor 3, C-terminal

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p12 Primary Assembly

    Range
    109309565..109397945 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005271100.2XP_005271157.1  sortilin isoform X1

    Conserved Domains (2) summary
    smart00602
    Location:133740
    VPS10; VPS10 domain
    pfam15901
    Location:573740
    Sortilin_C; Sortilin, neurotensin receptor 3, C-terminal
  2. XM_006710812.2XP_006710875.1  sortilin isoform X2

    See identical proteins and their annotated locations for XP_006710875.1

    Conserved Domains (2) summary
    smart00602
    Location:1605
    VPS10; VPS10 domain
    pfam15901
    Location:438605
    Sortilin_C; Sortilin, neurotensin receptor 3, C-terminal
  3. XM_005271101.3XP_005271158.1  sortilin isoform X2

    See identical proteins and their annotated locations for XP_005271158.1

    Conserved Domains (2) summary
    smart00602
    Location:1605
    VPS10; VPS10 domain
    pfam15901
    Location:438605
    Sortilin_C; Sortilin, neurotensin receptor 3, C-terminal
  4. XM_005271102.2XP_005271159.1  sortilin isoform X2

    See identical proteins and their annotated locations for XP_005271159.1

    Conserved Domains (2) summary
    smart00602
    Location:1605
    VPS10; VPS10 domain
    pfam15901
    Location:438605
    Sortilin_C; Sortilin, neurotensin receptor 3, C-terminal
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