This gene encodes a protein with a putative role in the localization of trans-Golgi network (TGN) membrane proteins. Mouse and rat homologs have been identified and studies of the homologous rat protein indicate a role in directing TGN localization of furin by binding to the protease's phosphorylated cytosolic domain. In addition, the human protein plays a role in HIV-1 Nef-med... See more...

Aliases for PACS1 Gene

Aliases for PACS1 Gene

  • Phosphofurin Acidic Cluster Sorting Protein 1 2 3 4 5
  • KIAA1175 2 4
  • PACS-1 3 4
  • Cytosolic Sorting Protein PACS-1 3
  • FLJ10209 2
  • MRD17 3
  • PACS1 5
  • SHMS 3

External Ids for PACS1 Gene

Previous GeneCards Identifiers for PACS1 Gene

  • GC11P067519
  • GC11P066088
  • GC11P065613
  • GC11P065595
  • GC11P065837
  • GC11P062163
  • GC11P066071

Summaries for PACS1 Gene

Entrez Gene Summary for PACS1 Gene

  • This gene encodes a protein with a putative role in the localization of trans-Golgi network (TGN) membrane proteins. Mouse and rat homologs have been identified and studies of the homologous rat protein indicate a role in directing TGN localization of furin by binding to the protease's phosphorylated cytosolic domain. In addition, the human protein plays a role in HIV-1 Nef-mediated downregulation of cell surface MHC-I molecules to the TGN, thereby enabling HIV-1 to escape immune surveillance. [provided by RefSeq, Jul 2008]

GeneCards Summary for PACS1 Gene

PACS1 (Phosphofurin Acidic Cluster Sorting Protein 1) is a Protein Coding gene. Diseases associated with PACS1 include Schuurs-Hoeijmakers Syndrome and Horseshoe Kidney. Among its related pathways are Nef-mediates down modulation of cell surface receptors by recruiting them to clathrin adapters and HIV Life Cycle. Gene Ontology (GO) annotations related to this gene include ion channel binding. An important paralog of this gene is PACS2.

UniProtKB/Swiss-Prot Summary for PACS1 Gene

  • Coat protein that is involved in the localization of trans-Golgi network (TGN) membrane proteins that contain acidic cluster sorting motifs. Controls the endosome-to-Golgi trafficking of furin and mannose-6-phosphate receptor by connecting the acidic-cluster-containing cytoplasmic domain of these molecules with the adapter-protein complex-1 (AP-1) of endosomal clathrin-coated membrane pits. Involved in HIV-1 nef-mediated removal of MHC-I from the cell surface to the TGN.

Gene Wiki entry for PACS1 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PACS1 Gene

Genomics for PACS1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for PACS1 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PACS1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PACS1

Top Transcription factor binding sites by QIAGEN in the PACS1 gene promoter:
  • AP-1
  • ATF-2
  • c-Jun
  • c-Myc
  • Evi-1
  • FOXO4
  • Max1
  • p300
  • RFX1
  • RREB-1

Genomic Locations for PACS1 Gene

Latest Assembly
chr11:66,070,272-66,244,744
(GRCh38/hg38)
Size:
174,473 bases
Orientation:
Plus strand

Previous Assembly
chr11:65,837,743-66,012,215
(GRCh37/hg19 by Entrez Gene)
Size:
174,473 bases
Orientation:
Plus strand

chr11:65,837,834-66,012,218
(GRCh37/hg19 by Ensembl)
Size:
174,385 bases
Orientation:
Plus strand

Genomic View for PACS1 Gene

Genes around PACS1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PACS1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PACS1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PACS1 Gene

Proteins for PACS1 Gene

  • Protein details for PACS1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q6VY07-PACS1_HUMAN
    Recommended name:
    Phosphofurin acidic cluster sorting protein 1
    Protein Accession:
    Q6VY07
    Secondary Accessions:
    • Q6PJY6
    • Q6PKB6
    • Q7Z590
    • Q7Z5W4
    • Q8N8K6
    • Q96MW0
    • Q9NW92
    • Q9ULP5

    Protein attributes for PACS1 Gene

    Size:
    963 amino acids
    Molecular mass:
    104898 Da
    Quaternary structure:
    • Associates with AP-1 and AP-3 but not with AP-2 complexes (PubMed:11331585). Interacts with FURIN (By similarity). Forms a ternary complex with FURIN and AP-1 (PubMed:11331585). Interacts with NPHP1; the interaction is dependent of NPHP1 phosphorylation by CK2 (PubMed:16308564). Interacts with PKD2 (via acidic region) (PubMed:15692563). Interacts with SORL1 (PubMed:17855360, PubMed:17646382).
    • (Microbial infection) Interacts with HIV-1 Nef.
    • (Microbial infection) Interacts with Epstein-barr virus protein BBLF1.
    SequenceCaution:
    • Sequence=AAH09936.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305}; Sequence=BAB71164.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};

    Alternative splice isoforms for PACS1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PACS1 Gene

Post-translational modifications for PACS1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Antibodies for research

  • Abcam antibodies for PACS1
  • Santa Cruz Biotechnology (SCBT) Antibodies for PACS1

No data available for DME Specific Peptides for PACS1 Gene

Domains & Families for PACS1 Gene

Gene Families for PACS1 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for PACS1 Gene

Suggested Antigen Peptide Sequences for PACS1 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ58767, highly similar to Phosphofurin acidic cluster sorting protein 1 (B4DF77_HUMAN)
  • Phosphofurin acidic cluster sorting protein 1 (PACS1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q6VY07

UniProtKB/Swiss-Prot:

PACS1_HUMAN :
  • Belongs to the PACS family.
Family:
  • Belongs to the PACS family.
genes like me logo Genes that share domains with PACS1: view

Function for PACS1 Gene

Molecular function for PACS1 Gene

UniProtKB/Swiss-Prot Function:
Coat protein that is involved in the localization of trans-Golgi network (TGN) membrane proteins that contain acidic cluster sorting motifs. Controls the endosome-to-Golgi trafficking of furin and mannose-6-phosphate receptor by connecting the acidic-cluster-containing cytoplasmic domain of these molecules with the adapter-protein complex-1 (AP-1) of endosomal clathrin-coated membrane pits. Involved in HIV-1 nef-mediated removal of MHC-I from the cell surface to the TGN.

Phenotypes From GWAS Catalog for PACS1 Gene

Gene Ontology (GO) - Molecular Function for PACS1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 10707087
GO:0044325 ion channel binding IPI 15692563
genes like me logo Genes that share ontologies with PACS1: view
genes like me logo Genes that share phenotypes with PACS1: view

Human Phenotype Ontology for PACS1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PACS1

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for PACS1 Gene

Localization for PACS1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PACS1 Gene

Golgi apparatus, trans-Golgi network. Note=Localizes in the perinuclear region, probably the TGN. {ECO:0000305 PubMed:11331585}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PACS1 gene
Compartment Confidence
cytosol 5
golgi apparatus 4
nucleus 3
plasma membrane 2
cytoskeleton 2
endosome 2
lysosome 2
extracellular 1
mitochondrion 1
endoplasmic reticulum 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Microtubules (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PACS1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005794 Golgi apparatus IEA --
GO:0005829 cytosol TAS --
GO:0030137 COPI-coated vesicle IEA --
genes like me logo Genes that share ontologies with PACS1: view

Pathways & Interactions for PACS1 Gene

genes like me logo Genes that share pathways with PACS1: view

SIGNOR curated interactions for PACS1 Gene

Is activated by:

Gene Ontology (GO) - Biological Process for PACS1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016032 viral process IEA --
GO:0034067 protein localization to Golgi apparatus IEA --
GO:0050690 regulation of defense response to virus by virus TAS --
GO:0072659 protein localization to plasma membrane IMP 15692563
genes like me logo Genes that share ontologies with PACS1: view

Drugs & Compounds for PACS1 Gene

(1) Drugs for PACS1 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Mannose 6-phosphate Investigational Pharma 0
genes like me logo Genes that share compounds with PACS1: view

Transcripts for PACS1 Gene

mRNA/cDNA for PACS1 Gene

1 REFSEQ mRNAs :
15 NCBI additional mRNA sequence :
16 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PACS1

Alternative Splicing Database (ASD) splice patterns (SP) for PACS1 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7a · 7b ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14a · 14b ^ 15 ^ 16a · 16b ^ 17 ^ 18 ^ 19 ^ 20a · 20b ^ 21 ^ 22a ·
SP1: - - - -
SP2:
SP3:
SP4: -
SP5:
SP6:

ExUns: 22b · 22c · 22d ^ 23 ^ 24a · 24b
SP1:
SP2:
SP3:
SP4:
SP5:
SP6: -

Relevant External Links for PACS1 Gene

GeneLoc Exon Structure for
PACS1

Expression for PACS1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PACS1 Gene

mRNA differential expression in normal tissues according to GTEx for PACS1 Gene

This gene is overexpressed in Whole Blood (x4.2).

Protein differential expression in normal tissues from HIPED for PACS1 Gene

This gene is overexpressed in Brain (10.8), Tlymphocyte (8.2), and Peripheral blood mononuclear cells (6.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for PACS1 Gene



Protein tissue co-expression partners for PACS1 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PACS1

SOURCE GeneReport for Unigene cluster for PACS1 Gene:

Hs.644326

Evidence on tissue expression from TISSUES for PACS1 Gene

  • Nervous system(4.8)
  • Kidney(4.4)
  • Liver(4.3)
  • Skin(2.1)
  • Intestine(2.1)
  • Blood(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for PACS1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • integumentary
  • nervous
  • reproductive
  • skeleton
Regions:
Head and neck:
  • brain
  • ear
  • eye
  • eyelid
  • face
  • forehead
  • head
  • lip
  • nose
  • outer ear
  • scalp
  • skull
Thorax:
  • breast
Abdomen:
  • intestine
  • large intestine
  • small intestine
Pelvis:
  • testicle
  • uterus
Limb:
  • foot
  • lower limb
General:
  • blood
  • blood vessel
  • hair
  • skin
genes like me logo Genes that share expression patterns with PACS1: view

Primer products for research

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA Expression by UniProt/SwissProt for PACS1 Gene

Orthologs for PACS1 Gene

This gene was present in the common ancestor of animals.

Orthologs for PACS1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia PACS1 29 30
  • 99.83 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia PACS1 29 30
  • 92.34 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia PACS1 29 30
  • 91.72 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Pacs1 29 16 30
  • 89.84 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Pacs1 29
  • 89.18 (n)
Oppossum
(Monodelphis domestica)
Mammalia PACS1 30
  • 67 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia PACS1 30
  • 34 (a)
OneToOne
Chicken
(Gallus gallus)
Aves PACS1 29 30
  • 66.47 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia PACS1 30
  • 78 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia LOC100490541 29
  • 64.48 (n)
Str.5177 29
Zebrafish
(Danio rerio)
Actinopterygii pacs1a 29 30
  • 67.91 (n)
OneToMany
PACS1 (1 of 6) 30
  • 67 (a)
OneToMany
PACS1 (6 of 6) 30
  • 67 (a)
OneToMany
PACS1 (5 of 6) 30
  • 60 (a)
OneToMany
PACS1 (3 of 6) 30
  • 57 (a)
OneToMany
PACS1 (4 of 6) 30
  • 48 (a)
OneToMany
Fruit Fly
(Drosophila melanogaster)
Insecta KrT95D 30
  • 25 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea tag-232 30
  • 24 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 30
  • 34 (a)
OneToMany
Species where no ortholog for PACS1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for PACS1 Gene

ENSEMBL:
Gene Tree for PACS1 (if available)
TreeFam:
Gene Tree for PACS1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PACS1: view image
Alliance of Genome Resources:
Additional Orthologs for PACS1

Paralogs for PACS1 Gene

Paralogs for PACS1 Gene

(1) SIMAP similar genes for PACS1 Gene using alignment to 11 proteins:

  • PACS1_HUMAN
  • B4DF77_HUMAN
  • E9PNG7_HUMAN
  • E9PNZ9_HUMAN
  • E9PPK2_HUMAN
  • E9PSE1_HUMAN
  • E9PSG7_HUMAN
  • H0YCU5_HUMAN
  • H0YE62_HUMAN
  • H0YF56_HUMAN
  • Q9NTH2_HUMAN
genes like me logo Genes that share paralogs with PACS1: view

Variants for PACS1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PACS1 Gene

SNP ID Clinical significance and condition Chr 11 pos Variation AA Info Type
1012800 Likely Benign: not provided 66,230,809(+) G/A
NM_018026.4(PACS1):c.1495G>A (p.Val499Met)
MISSENSE
1012801 Likely Benign: not provided 66,241,613(+) C/T
NM_018026.4(PACS1):c.2616C>T (p.Thr872=)
SYNONYMOUS
1032016 Uncertain Significance: Schuurs-hoeijmakers syndrome 66,216,104(+) T/A
NM_018026.4(PACS1):c.661-15T>A
INTRON
928564 Uncertain Significance: not specified 66,227,549(+) A/T
NM_018026.4(PACS1):c.1339A>T (p.Asn447Tyr)
MISSENSE
945180 Uncertain Significance: Schuurs-hoeijmakers syndrome 66,243,036(+) G/C
NM_018026.4(PACS1):c.2776+5G>C
INTRON

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for PACS1 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for PACS1 Gene

Variant ID Type Subtype PubMed ID
dgv220e199 CNV deletion 23128226
esv1000442 OTHER inversion 20482838
esv25273 CNV loss 19812545
esv2660282 CNV deletion 23128226
esv2661166 CNV deletion 23128226
esv2668639 CNV deletion 23128226
esv2744636 CNV deletion 23290073
esv3303782 CNV mobile element insertion 20981092
esv3305790 CNV mobile element insertion 20981092
esv3308818 CNV mobile element insertion 20981092
esv3323893 CNV insertion 20981092
esv3355386 CNV insertion 20981092
esv3445468 CNV insertion 20981092
esv3626686 CNV loss 21293372
esv3626687 CNV loss 21293372
esv3626688 CNV loss 21293372
nsv1122635 CNV deletion 24896259
nsv1127201 CNV deletion 24896259
nsv1143544 CNV deletion 24896259
nsv362 CNV deletion 18451855
nsv498760 CNV loss 21111241
nsv514631 CNV loss 21397061
nsv517090 CNV loss 19592680
nsv555222 CNV loss 21841781
nsv818843 CNV loss 17921354

Variation tolerance for PACS1 Gene

Residual Variation Intolerance Score: 4.08% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.33; 26.42% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PACS1 Gene

Human Gene Mutation Database (HGMD)
PACS1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PACS1
Leiden Open Variation Database (LOVD)
PACS1

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PACS1 Gene

Disorders for PACS1 Gene

MalaCards: The human disease database

(16) MalaCards diseases for PACS1 Gene - From: OMI, CVR, GTR, ORP, SWI, COP, and GCD

- elite association - COSMIC cancer census association via MalaCards
Search PACS1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

PACS1_HUMAN
  • Schuurs-Hoeijmakers syndrome (SHMS) [MIM:615009]: A syndromic form of mental retardation, a disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. SHMS patients have intellectual disability in combination with distinct craniofacial features and genital abnormalities. {ECO:0000269 PubMed:23159249}. Note=The disease is caused by variants affecting the gene represented in this entry.

Additional Disease Information for PACS1

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with PACS1: view

No data available for Genatlas for PACS1 Gene

Publications for PACS1 Gene

  1. Recurrent de novo mutations in PACS1 cause defective cranial-neural-crest migration and define a recognizable intellectual-disability syndrome. (PMID: 23159249) Schuurs-Hoeijmakers JH … Brunner HG (American journal of human genetics 2012) 3 4 72
  2. Trafficking of TRPP2 by PACS proteins represents a novel mechanism of ion channel regulation. (PMID: 15692563) Köttgen M … Walz G (The EMBO journal 2005) 3 4 22
  3. Phosphorylation by casein kinase 2 induces PACS-1 binding of nephrocystin and targeting to cilia. (PMID: 16308564) Schermer B … Benzing T (The EMBO journal 2005) 3 4 22
  4. Signaling but not trafficking function of HIV-1 protein Nef is essential for Nef-induced defects in human intrathymic T-cell development. (PMID: 12855553) Stove V … Verhasselt B (Blood 2003) 2 3 22
  5. AP-1 recruitment to VAMP4 is modulated by phosphorylation-dependent binding of PACS-1. (PMID: 14608369) Hinners I … Tooze SA (EMBO reports 2003) 2 3 22

Products for PACS1 Gene

Sources for PACS1 Gene