Human Gene AP4S1 (ENST00000542754.7_6) from GENCODE V47lift37
  Description: adaptor related protein complex 4 subunit sigma 1, transcript variant 2 (from RefSeq NM_001128126.3)
Gencode Transcript: ENST00000542754.7_6
Gencode Gene: ENSG00000100478.17_17
Transcript (Including UTRs)
   Position: hg19 chr14:31,494,855-31,565,656 Size: 70,802 Total Exon Count: 6 Strand: +
Coding Region
   Position: hg19 chr14:31,535,403-31,562,241 Size: 26,839 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesGeneReviewsModel Information
Methods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr14:31,494,855-31,565,656)mRNA (may differ from genome)Protein (144 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: AP4S1_HUMAN
DESCRIPTION: RecName: Full=AP-4 complex subunit sigma-1; AltName: Full=AP-4 adapter complex subunit sigma-1; AltName: Full=Adapter-related protein complex 4 subunit sigma-1; AltName: Full=Sigma-1 subunit of AP-4; AltName: Full=Sigma-4-adaptin; Short=Sigma4-adaptin;
FUNCTION: Subunit of novel type of clathrin- or non-clathrin- associated protein coat involved in targeting proteins from the trans-Golgi network (TGN) to the endosomal-lysosomal system.
SUBUNIT: Adapter-like complex 4 (AP-4) is a heterotetramer composed of two large adaptins (epsilon-type subunit AP4E1 and beta-type subunitAP4B1), a medium adaptin (mu-type subunit AP4M1) and a small adaptin (sigma-type AP4S1).
SUBCELLULAR LOCATION: Golgi apparatus, trans-Golgi network. Membrane, coated pit. Note=Associated with the trans-Golgi network. Found in soma and dendritic shafts of neuronal cells.
TISSUE SPECIFICITY: Widely expressed.
DISEASE: Defects in AP4S1 are the cause of cerebral palsy spastic quadriplegic type 6 (CPSQ6) [MIM:614067]. CPSQ6 is a neurodevelopmental disorder characterized by neonatal hypotonia that progresses to hypertonia and spasticity, and severe mental retardation with poor or absent speech development.
SIMILARITY: Belongs to the adaptor complexes small subunit family.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: AP4S1
Diseases sorted by gene-association score: spastic paraplegia 52, autosomal recessive* (927), severe intellectual disability and progressive spastic paraplegia* (350), spastic paraplegia 52* (119), hereditary spastic paraplegia 51 (17), cerebral palsy (10), spastic paraplegia 50, autosomal recessive (10), spastic paraplegia 28, autosomal recessive (10), spastic paraplegia 56, autosomal recessive (8), spastic paraplegia 47, autosomal recessive (7), spastic paraplegia 54, autosomal recessive (7), spastic paraplegia 18, autosomal recessive (7)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 3.85 RPKM in Testis
Total median expression: 70.01 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -59.60210-0.284 Picture PostScript Text
3' UTR -1542.803415-0.452 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR016635 - AP_complex_ssu
IPR022775 - AP_mu_sigma_su
IPR011012 - Longin-like_dom

Pfam Domains:
PF01217 - Clathrin adaptor complex small chain

SCOP Domains:
64356 - SNARE-like

ModBase Predicted Comparative 3D Structure on Q9Y587
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Biological Process:
GO:0006605 protein targeting
GO:0008104 protein localization
GO:0015031 protein transport

Cellular Component:
GO:0005794 Golgi apparatus
GO:0016020 membrane
GO:0030124 AP-4 adaptor complex
GO:0031904 endosome lumen
GO:0032588 trans-Golgi network membrane
GO:0043231 intracellular membrane-bounded organelle


-  Descriptions from all associated GenBank mRNAs
  AK316517 - Homo sapiens cDNA, FLJ79416 complete cds, highly similar to Adapter-relatedprotein complex 4 sigma- 1 subunit.
AK304115 - Homo sapiens cDNA FLJ50952 complete cds, highly similar to Adapter-relatedprotein complex 4 sigma- 1 subunit.
AB030654 - Homo sapiens mRNA for AP-4 clathrin adaptor-related complex sigma4 subunit, complete cds.
BX247969 - human full-length cDNA clone CS0DF007YL16 of Fetal brain of Homo sapiens (human).
AF155159 - Homo sapiens adaptor-related protein complex AP-4 sigma4 subunit mRNA, complete cds.
BC001259 - Homo sapiens adaptor-related protein complex 4, sigma 1 subunit, mRNA (cDNA clone MGC:5011 IMAGE:3454117), complete cds.
JD142876 - Sequence 123900 from Patent EP1572962.
JD553190 - Sequence 534214 from Patent EP1572962.
JD538194 - Sequence 519218 from Patent EP1572962.
JD214243 - Sequence 195267 from Patent EP1572962.
JD445979 - Sequence 427003 from Patent EP1572962.
BC035622 - Homo sapiens adaptor-related protein complex 4, sigma 1 subunit, mRNA (cDNA clone IMAGE:5171310), with apparent retained intron.
JD499028 - Sequence 480052 from Patent EP1572962.
BT006701 - Homo sapiens adaptor-related protein complex 4, sigma 1 subunit mRNA, complete cds.
DQ890707 - Synthetic construct clone IMAGE:100003337; FLH165332.01X; RZPDo839A12160D adaptor-related protein complex 4, sigma 1 subunit (AP4S1) gene, encodes complete protein.
DQ893891 - Synthetic construct Homo sapiens clone IMAGE:100008351; FLH165328.01L; RZPDo839A12159D adaptor-related protein complex 4, sigma 1 subunit (AP4S1) gene, encodes complete protein.
CR457100 - Homo sapiens full open reading frame cDNA clone RZPDo834A029D for gene AP4S1, adaptor-related protein complex 4, sigma 1 subunit; complete cds, incl. stopcodon.
JD426822 - Sequence 407846 from Patent EP1572962.
JD422120 - Sequence 403144 from Patent EP1572962.
JD567042 - Sequence 548066 from Patent EP1572962.
JD301094 - Sequence 282118 from Patent EP1572962.
JD242806 - Sequence 223830 from Patent EP1572962.
JD321242 - Sequence 302266 from Patent EP1572962.
JD388806 - Sequence 369830 from Patent EP1572962.
AK098330 - Homo sapiens cDNA FLJ41011 fis, clone UTERU2018514.
JD286738 - Sequence 267762 from Patent EP1572962.
JD043128 - Sequence 24152 from Patent EP1572962.
JD043129 - Sequence 24153 from Patent EP1572962.
JD284123 - Sequence 265147 from Patent EP1572962.
JD425286 - Sequence 406310 from Patent EP1572962.
JD425289 - Sequence 406313 from Patent EP1572962.
JD291771 - Sequence 272795 from Patent EP1572962.
JD291772 - Sequence 272796 from Patent EP1572962.
JD421944 - Sequence 402968 from Patent EP1572962.
JD446406 - Sequence 427430 from Patent EP1572962.
JD446407 - Sequence 427431 from Patent EP1572962.
JD340975 - Sequence 321999 from Patent EP1572962.
JD340974 - Sequence 321998 from Patent EP1572962.
JD525757 - Sequence 506781 from Patent EP1572962.
JD226345 - Sequence 207369 from Patent EP1572962.
JD381244 - Sequence 362268 from Patent EP1572962.
JD381245 - Sequence 362269 from Patent EP1572962.
JD130965 - Sequence 111989 from Patent EP1572962.
JD130966 - Sequence 111990 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9Y587 (Reactome details) participates in the following event(s):

R-HSA-5229132 AP4 binds APP
R-HSA-5229111 AP4 transports APP from trans-Golgi network to endosome lumen
R-HSA-432720 Lysosome Vesicle Biogenesis
R-HSA-421837 Clathrin derived vesicle budding
R-HSA-199992 trans-Golgi Network Vesicle Budding
R-HSA-199991 Membrane Trafficking
R-HSA-5653656 Vesicle-mediated transport

-  Other Names for This Gene
  Alternate Gene Symbols: AP4S1 , AP4S1_HUMAN, ENST00000542754.1, ENST00000542754.2, ENST00000542754.3, ENST00000542754.4, ENST00000542754.5, ENST00000542754.6, G3V2N8, NM_001128126, Q6IAQ4, Q86U36, Q9BVE7, Q9Y587, uc324ucs.1, uc324ucs.2
UCSC ID: ENST00000542754.7_6
RefSeq Accession: NM_001128126.3
Protein: Q9Y587 (aka AP4S1_HUMAN or A4S1_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene AP4S1:
ap4-def (AP-4-Associated Hereditary Spastic Paraplegia)
hsp (Hereditary Spastic Paraplegia Overview)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.