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PTCD3 pentatricopeptide repeat domain 3 [ Homo sapiens (human) ]

Gene ID: 55037, updated on 10-Dec-2024

Summary

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Official Symbol
PTCD3provided by HGNC
Official Full Name
pentatricopeptide repeat domain 3provided by HGNC
Primary source
HGNC:HGNC:24717
See related
Ensembl:ENSG00000132300 MIM:614918; AllianceGenome:HGNC:24717
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
mS39; COXPD51; MRP-S39
Summary
Enables rRNA binding activity and ribosomal small subunit binding activity. Involved in mitochondrial translation. Located in several cellular components, including cytosol; mitochondrion; and nucleoplasm. Implicated in combined oxidative phosphorylation deficiency 51. [provided by Alliance of Genome Resources, Dec 2024]
Expression
Ubiquitous expression in testis (RPKM 14.7), heart (RPKM 11.3) and 25 other tissues See more
Orthologs
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Genomic context

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See PTCD3 in Genome Data Viewer
Location:
2p11.2
Exon count:
24
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (86106235..86142157)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (86108305..86144223)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (86333358..86369280)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105374843 Neighboring gene CRISPRi-validated cis-regulatory element chr2.3134 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16149 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:86239243-86239743 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16150 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:86260844-86261047 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16151 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11710 Neighboring gene conserved acetylation island sequence 34 enhancer Neighboring gene RNA polymerase I subunit A Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:86272354-86273553 Neighboring gene MPRA-validated peak3776 silencer Neighboring gene MED14-independent group 3 enhancer GRCh37_chr2:86296595-86297794 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:86301664-86302164 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:86302165-86302665 Neighboring gene uncharacterized LOC124907852 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16152 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16153 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16154 Neighboring gene Sharpr-MPRA regulatory region 1812 Neighboring gene MPRA-validated peak3777 silencer Neighboring gene small nucleolar RNA, C/D box 94 Neighboring gene inner membrane mitochondrial protein Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16155 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16156 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16157 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16158 Neighboring gene microRNA 4779 Neighboring gene mitochondrial ribosomal protein L35

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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Related articles in PubMed

  1. Mitochondrial ribosomal protein PTCD3 mutations cause oxidative phosphorylation defects with Leigh syndrome. Borna NN, et al. Neurogenetics, 2019 Mar. PMID 30607703
  2. Elevated expression of PTCD3 correlates with tumor progression and predicts poor prognosis in patients with prostate cancer. Huang Y, et al. Mol Med Rep, 2018 Oct. PMID 30132530, Free PMC Article
  3. Leigh syndrome is the main clinical characteristic of PTCD3 deficiency. Muñoz-Pujol G, et al. Brain Pathol, 2023 May. PMID 36450274, Free PMC Article
  4. Pentatricopeptide repeat domain protein 3 associates with the mitochondrial small ribosomal subunit and regulates translation. Davies SM, et al. FEBS Lett, 2009 Jun 18. PMID 19427859
  5. Genome-wide association study of blood pressure response to methylphenidate treatment of attention-deficit/hyperactivity disorder. Mick E, et al. Prog Neuropsychopharmacol Biol Psychiatry, 2011 Mar 30. PMID 21130132

See all (146) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Leigh syndrome is the main clinical characteristic of PTCD3 deficiency.
    Title: Leigh syndrome is the main clinical characteristic of PTCD3 deficiency.
  2. Sanger sequencing of gDNA from the affected individual and unaffected family members confirming the PTCD3 variants
    Title: Mitochondrial ribosomal protein PTCD3 mutations cause oxidative phosphorylation defects with Leigh syndrome.
  3. PTCD3 levels may serve as a novel biomarker for prostate cancer prognosis.
    Title: Elevated expression of PTCD3 correlates with tumor progression and predicts poor prognosis in patients with prostate cancer.
  4. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
    Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
  5. Observational study of gene-disease association. (HuGE Navigator)
    Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
  6. lowering PTCD3 in 143B osteosarcoma cells decreased mitochondrial protein synthesis, mitochondrial respiration and the activity of Complexes III and IV, suggesting that PTCD3 has a role in mitochondrial translation
    Title: Pentatricopeptide repeat domain protein 3 associates with the mitochondrial small ribosomal subunit and regulates translation.
  7. PTCD3 associates with the small subunit of the mitochondrial ribosome and is required for efficient translation.
    Title: Pentatricopeptide repeat domain protein 3 associates with the mitochondrial small ribosomal subunit and regulates translation.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Combined oxidative phosphorylation deficiency 51
MedGen: C5436703 OMIM: 619057 GeneReviews: Not available
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EBI GWAS Catalog

Description
Genome-wide association study of blood pressure response to methylphenidate treatment of attention-deficit/hyperactivity disorder.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env Tandem affinity purification and mass spectrometry analysis identify pentatricopeptide repeat domain 3 (PTCD3), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Gag-Pol gag-pol Tandem affinity purification and mass spectrometry analysis identify pentatricopeptide repeat domain 3 (PTCD3), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Nef nef Tandem affinity purification and mass spectrometry analysis identify pentatricopeptide repeat domain 3 (PTCD3), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Pr55(Gag) gag Tandem affinity purification and mass spectrometry analysis identify pentatricopeptide repeat domain 3 (PTCD3), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ20758, DKFZp666K071

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding HDA PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables rRNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables rRNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables ribosomal small subunit binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables ribosomal small subunit binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in mitochondrial translation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in mitochondrial translation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in mitochondrial translation NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in regulation of translation IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in mitochondrial inner membrane NAS
Non-traceable Author Statement
more info
 PubMed 
located_in mitochondrial inner membrane TAS
Traceable Author Statement
more info
  
located_in mitochondrial matrix IDA
Inferred from Direct Assay
more info
 PubMed 
part_of mitochondrial small ribosomal subunit NAS
Non-traceable Author Statement
more info
 PubMed 
located_in mitochondrion HTP PubMed 
is_active_in mitochondrion IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in mitochondrion IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in plasma membrane IDA
Inferred from Direct Assay
more info
  

General protein information

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Preferred Names
small ribosomal subunit protein mS39
Names
28S ribosomal protein S39, mitochondrial
TRG-15
mitochondrial small ribosomal subunit protein mS39
pentatricopeptide repeat domain-containing protein 3, mitochondrial
pentatricopeptide repeat-containing protein 3, mitochondrial
transformation-related gene 15 protein

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.

mRNA and Protein(s)

  1. NM_017952.6 → NP_060422.4  small ribosomal subunit protein mS39 precursor

    See identical proteins and their annotated locations for NP_060422.4

    Status: VALIDATED

    Source sequence(s)
    AC009309, BC011832, BQ574414, DA479719
    Consensus CDS
    CCDS33235.1
    UniProtKB/Swiss-Prot
    A6NHD2, D6W5M1, Q597H0, Q658Y9, Q96EY7, Q9BUZ8, Q9NWL0
    Related
    ENSP00000254630.7, ENST00000254630.12
    Conserved Domains (3) summary
    sd00004
    Location:258 → 285
    PPR; PPR repeat [structural motif]
    pfam13812
    Location:319 → 379
    PPR_3; Pentatricopeptide repeat domain
    pfam13041
    Location:254 → 300
    PPR_2; PPR repeat family

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    86106235..86142157
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    86108305..86144223
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96EY7.3 GenPept UniProtKB/Swiss-Prot:Q96EY7

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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