Aliases for PTCD3 Gene

Aliases for PTCD3 Gene

  • Pentatricopeptide Repeat Domain 3 2 3 5
  • Pentatricopeptide Repeat Domain-Containing Protein 3, Mitochondrial 3 4
  • Mitochondrial Small Ribosomal Subunit Protein MS39 3 4
  • 28S Ribosomal Protein S39, Mitochondrial 3 4
  • Transformation-Related Gene 15 Protein 3 4
  • MRP-S39 3 4
  • TRG-15 3 4
  • Pentatricopeptide Repeat-Containing Protein 3, Mitochondrial 3
  • DKFZp666K071 2
  • FLJ20758 2
  • COXPD51 3
  • MRPS39 4
  • PTCD3 5

External Ids for PTCD3 Gene

Previous GeneCards Identifiers for PTCD3 Gene

  • GC02P086186
  • GC02P086333

Summaries for PTCD3 Gene

GeneCards Summary for PTCD3 Gene

PTCD3 (Pentatricopeptide Repeat Domain 3) is a Protein Coding gene. Diseases associated with PTCD3 include Combined Oxidative Phosphorylation Deficiency 51 and Ciliary Dyskinesia, Primary, 1. Among its related pathways are Mitochondrial translation and Organelle biogenesis and maintenance. Gene Ontology (GO) annotations related to this gene include ribosomal small subunit binding.

UniProtKB/Swiss-Prot Summary for PTCD3 Gene

  • Mitochondrial RNA-binding protein that has a role in mitochondrial translation.

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PTCD3 Gene

Genomics for PTCD3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for PTCD3 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 PTCD3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PTCD3

Top Transcription factor binding sites by QIAGEN in the PTCD3 gene promoter:
  • AML1a
  • AREB6
  • c-Rel
  • ER-alpha
  • HTF
  • Ik-2
  • Lmo2
  • Nkx2-5
  • p53
  • SEF-1 (1)

Genomic Locations for PTCD3 Gene

Latest Assembly
chr2:86,106,223-86,142,157
(GRCh38/hg38)
Size:
35,935 bases
Orientation:
Plus strand

Previous Assembly
chr2:86,333,358-86,369,280
(GRCh37/hg19 by Entrez Gene)
Size:
35,923 bases
Orientation:
Plus strand

chr2:86,333,305-86,369,280
(GRCh37/hg19 by Ensembl)
Size:
35,976 bases
Orientation:
Plus strand

Genomic View for PTCD3 Gene

Genes around PTCD3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PTCD3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PTCD3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PTCD3 Gene

Proteins for PTCD3 Gene

  • Protein details for PTCD3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96EY7-PTCD3_HUMAN
    Recommended name:
    Pentatricopeptide repeat domain-containing protein 3, mitochondrial
    Protein Accession:
    Q96EY7
    Secondary Accessions:
    • A6NHD2
    • D6W5M1
    • Q597H0
    • Q658Y9
    • Q9BUZ8
    • Q9NWL0

    Protein attributes for PTCD3 Gene

    Size:
    689 amino acids
    Molecular mass:
    78550 Da
    Quaternary structure:
    • Component of the mitochondrial small ribosomal subunit (mt-SSU). Mature mammalian 55S mitochondrial ribosomes consist of a small (28S) and a large (39S) subunit. The 28S small subunit contains a 12S ribosomal RNA (12S mt-rRNA) and 30 different proteins. The 39S large subunit contains a 16S rRNA (16S mt-rRNA), a copy of mitochondrial valine transfer RNA (mt-tRNA(Val)), which plays an integral structural role, and 52 different proteins. Associated with the 12S mitochondrial rRNA (12S mt-rRNA).

    Three dimensional structures from OCA and Proteopedia for PTCD3 Gene

    Alternative splice isoforms for PTCD3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PTCD3 Gene

Post-translational modifications for PTCD3 Gene

  • Ubiquitination at Lys67 and Lys126
  • Modification sites at PhosphoSitePlus

Other Protein References for PTCD3 Gene

No data available for DME Specific Peptides for PTCD3 Gene

Domains & Families for PTCD3 Gene

Gene Families for PTCD3 Gene

Protein Domains for PTCD3 Gene

Suggested Antigen Peptide Sequences for PTCD3 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ57349 (B4DF73_HUMAN)
  • Transformation-related gene 15 protein (PTCD3_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q96EY7

UniProtKB/Swiss-Prot:

PTCD3_HUMAN :
  • Belongs to the mitochondrion-specific ribosomal protein mS39 family.
Family:
  • Belongs to the mitochondrion-specific ribosomal protein mS39 family.
genes like me logo Genes that share domains with PTCD3: view

Function for PTCD3 Gene

Molecular function for PTCD3 Gene

UniProtKB/Swiss-Prot Function:
Mitochondrial RNA-binding protein that has a role in mitochondrial translation.

Phenotypes From GWAS Catalog for PTCD3 Gene

Gene Ontology (GO) - Molecular Function for PTCD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IEA,HDA 22658674
GO:0005515 protein binding IPI 21516116
GO:0019843 rRNA binding IBA,IDA 19427859
GO:0043024 ribosomal small subunit binding IBA,IDA 19427859
genes like me logo Genes that share ontologies with PTCD3: view
genes like me logo Genes that share phenotypes with PTCD3: view

Human Phenotype Ontology for PTCD3 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for PTCD3 Gene

MGI Knock Outs for PTCD3:
  • Ptcd3 Ptcd3<tm1.1(KOMP)Vlcg>

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PTCD3

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for PTCD3 Gene

Localization for PTCD3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PTCD3 Gene

Mitochondrion.

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 PTCD3 gene
Compartment Confidence
mitochondrion 5
nucleus 5
cytosol 5
plasma membrane 4

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for PTCD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005654 nucleoplasm IDA --
GO:0005739 mitochondrion IBA,IDA 19427859
GO:0005743 mitochondrial inner membrane TAS --
GO:0005829 cytosol IDA --
GO:0005840 ribosome IEA --
genes like me logo Genes that share ontologies with PTCD3: view

Pathways & Interactions for PTCD3 Gene

genes like me logo Genes that share pathways with PTCD3: view

Gene Ontology (GO) - Biological Process for PTCD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006417 regulation of translation IEA --
GO:0032543 mitochondrial translation IBA,IMP 19427859
GO:0070125 mitochondrial translational elongation TAS --
GO:0070126 mitochondrial translational termination TAS --
genes like me logo Genes that share ontologies with PTCD3: view

No data available for SIGNOR curated interactions for PTCD3 Gene

Drugs & Compounds for PTCD3 Gene

No Compound Related Data Available

Transcripts for PTCD3 Gene

mRNA/cDNA for PTCD3 Gene

1 REFSEQ mRNAs :
22 NCBI additional mRNA sequence :
20 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 PTCD3

Alternative Splicing Database (ASD) splice patterns (SP) for PTCD3 Gene

ExUns: 1a · 1b ^ 2 ^ 3a · 3b ^ 4a · 4b ^ 5 ^ 6a · 6b ^ 7a · 7b ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13a · 13b ^ 14a · 14b · 14c ^ 15a · 15b ^ 16a · 16b ·
SP1: - - - - - - -
SP2: - - - - -
SP3: - -
SP4:
SP5: -
SP6:
SP7:
SP8: - -
SP9:
SP10:
SP11: - -
SP12:
SP13:
SP14:
SP15:

ExUns: 16c ^ 17 ^ 18a · 18b ^ 19 ^ 20a · 20b ^ 21a · 21b ^ 22 ^ 23a · 23b · 23c ^ 24a · 24b ^ 25 ^ 26a · 26b
SP1: - - - - - - -
SP2: - - - - - - -
SP3: - - - -
SP4:
SP5:
SP6: -
SP7: - - -
SP8:
SP9: - - -
SP10: -
SP11:
SP12:
SP13:
SP14:
SP15: - -

Relevant External Links for PTCD3 Gene

GeneLoc Exon Structure for
PTCD3

Expression for PTCD3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PTCD3 Gene

Protein differential expression in normal tissues from HIPED for PTCD3 Gene

This gene is overexpressed in Breast (32.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for PTCD3 Gene



Protein tissue co-expression partners for PTCD3 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PTCD3

SOURCE GeneReport for Unigene cluster for PTCD3 Gene:

Hs.323489

mRNA Expression by UniProt/SwissProt for PTCD3 Gene:

Q96EY7-PTCD3_HUMAN
Tissue specificity: Abundant in testes, skeletal muscle and heart tissue.

Evidence on tissue expression from TISSUES for PTCD3 Gene

  • Nervous system(4.8)
  • Liver(4.7)
  • Lung(4.5)
  • Stomach(4.3)
  • Eye(4.3)
  • Intestine(2.9)
  • Kidney(2.5)
genes like me logo Genes that share expression patterns with PTCD3: view

Primer products for research

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for PTCD3 Gene

Orthologs for PTCD3 Gene

This gene was present in the common ancestor of animals.

Orthologs for PTCD3 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia PTCD3 29 30
  • 99.18 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia PTCD3 29 30
  • 85.75 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia PTCD3 29 30
  • 84.01 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Ptcd3 29
  • 80.95 (n)
Mouse
(Mus musculus)
Mammalia Ptcd3 29 16 30
  • 80.72 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia PTCD3 30
  • 62 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia PTCD3 30
  • 62 (a)
OneToOne
Chicken
(Gallus gallus)
Aves PTCD3 29 30
  • 60.65 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia PTCD3 30
  • 52 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia ptcd3 29
  • 58.68 (n)
Str.4806 29
Zebrafish
(Danio rerio)
Actinopterygii ptcd3 29 30
  • 59.73 (n)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta CG4679 29 30
  • 45.11 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP009772 29
  • 42.59 (n)
Worm
(Caenorhabditis elegans)
Secernentea Y110A7A.19 30
  • 20 (a)
OneToOne
Species where no ortholog for PTCD3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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 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)

Evolution for PTCD3 Gene

ENSEMBL:
Gene Tree for PTCD3 (if available)
TreeFam:
Gene Tree for PTCD3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PTCD3: view image
Alliance of Genome Resources:
Additional Orthologs for PTCD3

Paralogs for PTCD3 Gene

Pseudogenes.org Pseudogenes for PTCD3 Gene

genes like me logo Genes that share paralogs with PTCD3: view

No data available for Paralogs for PTCD3 Gene

Variants for PTCD3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PTCD3 Gene

SNP ID Clinical significance and condition Chr 02 pos Variation AA Info Type
977568 Pathogenic: Primary ciliary dyskinesia 86,132,409(+) A/G
NM_017952.6(PTCD3):c.1358A>G (p.His453Arg)
MISSENSE
982042 Pathogenic: Combined oxidative phosphorylation deficiency 51 86,118,919(+) A/G
NM_017952.6(PTCD3):c.415-2A>G
SPLICE_ACCEPTOR
982043 Pathogenic: Combined oxidative phosphorylation deficiency 51 86,134,952(+) C/CCT
NM_017952.6(PTCD3):c.1746_1747dup (p.Phe583fs)
FRAMESHIFT
rs13393659 -- p.Ala2Val
rs2241433 -- p.Ser681Gly

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for PTCD3 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 PTCD3 Gene

Variant ID Type Subtype PubMed ID
dgv3885n100 CNV gain 25217958
dgv6946n54 CNV gain 21841781
dgv712e214 CNV gain 21293372
esv2751903 CNV gain 17911159
esv3388387 CNV duplication 20981092
esv3591540 CNV gain 21293372
nsv458563 CNV gain 19166990

Variation tolerance for PTCD3 Gene

Residual Variation Intolerance Score: 22% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.34; 70.78% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PTCD3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PTCD3
Leiden Open Variation Database (LOVD)
PTCD3

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PTCD3 Gene

Disorders for PTCD3 Gene

MalaCards: The human disease database

(5) MalaCards diseases for PTCD3 Gene - From: OMI, CVR, COP, and GCD

- elite association - COSMIC cancer census association via MalaCards
Search PTCD3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for PTCD3

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 PTCD3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PTCD3 Gene

Publications for PTCD3 Gene

  1. Mitochondrial ribosomal protein PTCD3 mutations cause oxidative phosphorylation defects with Leigh syndrome. (PMID: 30607703) Borna NN … Okazaki Y (Neurogenetics 2019) 3 72
  2. Identification and characterization of CHCHD1, AURKAIP1, and CRIF1 as new members of the mammalian mitochondrial ribosome. (PMID: 23908630) Koc EC … Koc H (Frontiers in physiology 2013) 3 4
  3. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PMID: 20877624) Hendrickson SL … O'Brien SJ (PloS one 2010) 3 40
  4. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey SD … DREAM investigators (Diabetes care 2010) 3 40
  5. Pentatricopeptide repeat domain protein 3 associates with the mitochondrial small ribosomal subunit and regulates translation. (PMID: 19427859) Davies SM … Filipovska A (FEBS letters 2009) 3 4

Products for PTCD3 Gene

Sources for PTCD3 Gene