Aliases for AP5S1 Gene

Aliases for AP5S1 Gene

  • Adaptor Related Protein Complex 5 Subunit Sigma 1 2 3 5
  • Adaptor Related Protein Complex 5 Sigma 1 Subunit 2 3
  • Adaptor-Related Protein Complex 5 Sigma Subunit 3 4
  • AP-5 Complex Subunit Sigma-1 3 4
  • C20orf29 3 4
  • Sigma5 3 4
  • Adaptor-Related Protein Complex 5, Sigma 1 Subunit 2
  • Adapter-Related Protein Complex 5 Sigma Subunit 3
  • Chromosome 20 Open Reading Frame 29 2
  • Protein C20orf29 3
  • FLJ11168 2
  • AP5S1 5

External Ids for AP5S1 Gene

Previous HGNC Symbols for AP5S1 Gene

  • C20orf29

Previous GeneCards Identifiers for AP5S1 Gene

  • GC20P003804

Summaries for AP5S1 Gene

GeneCards Summary for AP5S1 Gene

AP5S1 (Adaptor Related Protein Complex 5 Subunit Sigma 1) is a Protein Coding gene. Diseases associated with AP5S1 include Spastic Paraplegia 15, Autosomal Recessive and Spastic Paraplegia 48, Autosomal Recessive.

UniProtKB/Swiss-Prot Summary for AP5S1 Gene

  • As part of AP-5, a probable fifth adaptor protein complex it may be involved in endosomal transport. According to PubMed:20613862, it is required for efficient homologous recombination DNA double-strand break repair.

Additional gene information for AP5S1 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for AP5S1 Gene

Genomics for AP5S1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for AP5S1 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 AP5S1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for AP5S1

Genomic Locations for AP5S1 Gene

Genomic Locations for AP5S1 Gene
chr20:3,820,524-3,828,838
(GRCh38/hg38)
Size:
8,315 bases
Orientation:
Plus strand
chr20:3,801,171-3,805,954
(GRCh37/hg19)
Size:
4,784 bases
Orientation:
Plus strand

Genomic View for AP5S1 Gene

Genes around AP5S1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
AP5S1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for AP5S1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for AP5S1 Gene

Proteins for AP5S1 Gene

  • Protein details for AP5S1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NUS5-AP5S1_HUMAN
    Recommended name:
    AP-5 complex subunit sigma-1
    Protein Accession:
    Q9NUS5
    Secondary Accessions:
    • B3KSD0
    • D3DVY7

    Protein attributes for AP5S1 Gene

    Size:
    200 amino acids
    Molecular mass:
    22522 Da
    Quaternary structure:
    • Probably part of the adaptor protein complex 5 (AP-5) a tetramer composed of AP5B1, AP5M1, AP5S1 and AP5Z1. Interacts with ZFYVE26 and SPG11.

neXtProt entry for AP5S1 Gene

Post-translational modifications for AP5S1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for AP5S1 Gene

No data available for DME Specific Peptides for AP5S1 Gene

Domains & Families for AP5S1 Gene

Gene Families for AP5S1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for AP5S1 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for AP5S1 Gene

GenScript: Design optimal peptide antigens:
  • Protein C20orf29 (CT029_HUMAN)
genes like me logo Genes that share domains with AP5S1: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for AP5S1 Gene

Function for AP5S1 Gene

Molecular function for AP5S1 Gene

UniProtKB/Swiss-Prot Function:
As part of AP-5, a probable fifth adaptor protein complex it may be involved in endosomal transport. According to PubMed:20613862, it is required for efficient homologous recombination DNA double-strand break repair.

Phenotypes From GWAS Catalog for AP5S1 Gene

Gene Ontology (GO) - Molecular Function for AP5S1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 20613862
genes like me logo Genes that share ontologies with AP5S1: view
genes like me logo Genes that share phenotypes with AP5S1: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for AP5S1

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for AP5S1 Gene

Localization for AP5S1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for AP5S1 Gene

Cytoplasm, cytosol. Late endosome membrane. Peripheral membrane protein. Cytoplasmic side. Lysosome membrane. Peripheral membrane protein. Cytoplasmic side.

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 AP5S1 gene
Compartment Confidence
endosome 5
lysosome 5
nucleus 4
cytosol 4
extracellular 1
mitochondrion 1
plasma membrane 0
peroxisome 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (4)
  • Nucleoplasm (4)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for AP5S1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005654 nucleoplasm IDA --
GO:0005737 cytoplasm IEA --
GO:0005764 lysosome IBA,IDA 22022230
GO:0005765 lysosomal membrane IEA --
GO:0005768 endosome IEA --
genes like me logo Genes that share ontologies with AP5S1: view

Pathways & Interactions for AP5S1 Gene

PathCards logo

SuperPathways for AP5S1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for AP5S1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000724 double-strand break repair via homologous recombination IMP 20613862
GO:0006281 DNA repair IEA --
GO:0006974 cellular response to DNA damage stimulus IEA --
GO:0015031 protein transport IEA --
GO:0016197 endosomal transport IBA,IMP 22022230
genes like me logo Genes that share ontologies with AP5S1: view

No data available for Pathways by source and SIGNOR curated interactions for AP5S1 Gene

Drugs & Compounds for AP5S1 Gene

No Compound Related Data Available

Transcripts for AP5S1 Gene

mRNA/cDNA for AP5S1 Gene

3 REFSEQ mRNAs :
8 NCBI additional mRNA sequence :
5 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for AP5S1

Alternative Splicing Database (ASD) splice patterns (SP) for AP5S1 Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b ^ 3a · 3b ^ 4a · 4b · 4c · 4d · 4e
SP1: - - -
SP2: - - -
SP3: - -
SP4: - -
SP5: -
SP6: -

Relevant External Links for AP5S1 Gene

GeneLoc Exon Structure for
AP5S1

Expression for AP5S1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for AP5S1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for AP5S1 Gene

This gene is overexpressed in Bone (52.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for AP5S1 Gene



Protein tissue co-expression partners for AP5S1 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for AP5S1

SOURCE GeneReport for Unigene cluster for AP5S1 Gene:

Hs.104806
genes like me logo Genes that share expression patterns with AP5S1: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for AP5S1 Gene

Orthologs for AP5S1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for AP5S1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia AP5S1 30 31
  • 99.5 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia AP5S1 30 31
  • 87 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia AP5S1 30
  • 83.59 (n)
C20ORF29 31
  • 82 (a)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Ap5s1 30
  • 82.61 (n)
Mouse
(Mus musculus)
Mammalia Ap5s1 30 17 31
  • 82.13 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia AP5S1 31
  • 67 (a)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia AP5S1 31
  • 44 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia ap5s1 30
  • 52.55 (n)
Zebrafish
(Danio rerio)
Actinopterygii ap5s1 30 31
  • 53.3 (n)
OneToOne
Species where no ortholog for AP5S1 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)
  • Chicken (Gallus gallus)
  • 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)
  • Fruit Fly (Drosophila melanogaster)
  • 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)
  • Platypus (Ornithorhynchus anatinus)
  • 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 Squirt (Ciona savignyi)
  • 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)
  • Worm (Caenorhabditis elegans)

Evolution for AP5S1 Gene

ENSEMBL:
Gene Tree for AP5S1 (if available)
TreeFam:
Gene Tree for AP5S1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for AP5S1: view image

Paralogs for AP5S1 Gene

No data available for Paralogs for AP5S1 Gene

Variants for AP5S1 Gene

Additional dbSNP identifiers (rs#s) for AP5S1 Gene

Structural Variations from Database of Genomic Variants (DGV) for AP5S1 Gene

Variant ID Type Subtype PubMed ID
esv3645050 CNV loss 21293372
nsv828673 CNV gain 20364138
nsv833899 CNV loss 17160897

Variation tolerance for AP5S1 Gene

Residual Variation Intolerance Score: 54.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.44; 42.96% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for AP5S1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
AP5S1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for AP5S1 Gene

Disorders for AP5S1 Gene

MalaCards: The human disease database

(3) MalaCards diseases for AP5S1 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
spastic paraplegia 15, autosomal recessive
  • spg15
spastic paraplegia 48, autosomal recessive
  • spg48
hereditary spastic paraplegia
  • spastic paraplegia 3, autosomal dominant
- elite association - COSMIC cancer census association via MalaCards
Search AP5S1 in MalaCards View complete list of genes associated with diseases
genes like me logo Genes that share disorders with AP5S1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for AP5S1 Gene

Publications for AP5S1 Gene

  1. The fifth adaptor protein complex. (PMID: 22022230) Hirst J … Robinson MS (PLoS biology 2011) 2 3 4
  2. The DNA sequence and comparative analysis of human chromosome 20. (PMID: 11780052) Deloukas P … Rogers J (Nature 2001) 2 3 4
  3. A genome-scale DNA repair RNAi screen identifies SPG48 as a novel gene associated with hereditary spastic paraplegia. (PMID: 20613862) Słabicki M … Buchholz F (PLoS biology 2010) 3 4
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4

Products for AP5S1 Gene

Sources for AP5S1 Gene