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SORT1 sortilin 1 [ Homo sapiens (human) ]

Gene ID: 6272, updated on 25-Nov-2021

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
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Genomic context

See SORT1 in Genome Data Viewer
Location:
1p13.3; 1p21.3-p13.1
Exon count:
23
Annotation release Status Assembly Chr Location
109.20211119 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (109309575..109397940, complement)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (109852197..109940540, 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 20S 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 Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
A genome-wide association study in Europeans and South Asians identifies five new loci for coronary artery disease.
GeneReviews: Not available
Biological, clinical and population relevance of 95 loci for blood lipids.
GeneReviews: Not available
Common variants at 30 loci contribute to polygenic dyslipidemia.
GeneReviews: Not available
Discovery and refinement of loci associated with lipid levels.
GeneReviews: Not available
Genome-wide association analysis of metabolic traits in a birth cohort from a founder population.
GeneReviews: Not available
Genome-wide association of early-onset myocardial infarction with single nucleotide polymorphisms and copy number variants.
GeneReviews: Not available
Genome-wide association of lipid-lowering response to statins in combined study populations.
GeneReviews: Not available
Genome-wide association study evaluating lipoprotein-associated phospholipase A2 mass and activity at baseline and after rosuvastatin therapy.
GeneReviews: Not available
Genome-wide association study of coronary heart disease and its risk factors in 8,090 African Americans: the NHLBI CARe Project.
GeneReviews: Not available
Genome-wide screen identifies rs646776 near sortilin as a regulator of progranulin levels in human plasma.
GeneReviews: Not available
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.
GeneReviews: Not available
Large-scale association analysis identifies 13 new susceptibility loci for coronary artery disease.
GeneReviews: Not available
Large-scale genome-wide association studies in East Asians identify new genetic loci influencing metabolic traits.
GeneReviews: Not available
Low density lipoprotein cholesterol level quantitative trait locus 6
MedGen: C3150834 OMIM: 613589 GeneReviews: Not available
Compare labs
New loci associated with kidney function and chronic kidney disease.
GeneReviews: Not available
Newly identified loci that influence lipid concentrations and risk of coronary artery disease.
GeneReviews: Not available
Shared genetic susceptibility to ischemic stroke and coronary artery disease: a genome-wide analysis of common variants.
GeneReviews: Not available
Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans.
GeneReviews: Not available

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 PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

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

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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_028280.1 RefSeqGene

    Range
    5024..93367
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001205228.2NP_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)
    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, ENST00000256637.8
    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 Updated Annotation Release 109.20211119

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    109309575..109397940 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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