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

Summary

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, Nov 2024]
Expression: Ubiquitous expression in testis (RPKM 14.7), heart (RPKM 11.3) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

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_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Leigh syndrome is the main clinical characteristic of PTCD3 deficiency.
Title: Leigh syndrome is the main clinical characteristic of PTCD3 deficiency.
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.
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.
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.
Observational study of gene-disease association. (HuGE Navigator)
Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
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.
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.

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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	not available

EBI GWAS Catalog

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

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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

WI-15372 (e-PCR)
- UniSTS:50951

RH45713 (e-PCR)
- UniSTS:50952

G19971 (e-PCR)
- UniSTS:11030

A001W01 (e-PCR)
- UniSTS:11031

RH12062 (e-PCR)
- UniSTS:16721

RH48137 (e-PCR)
- UniSTS:53090

D6S1615 (e-PCR)
- UniSTS:67967

SHGC-37694 (e-PCR)
- UniSTS:32900

D6S1615 (e-PCR)
- UniSTS:480396

SHGC-31152 (e-PCR)
- UniSTS:35741

RH36411 (e-PCR)
- UniSTS:39334

L18441 (e-PCR)
- UniSTS:71348

SHGC-132727 (e-PCR)
- UniSTS:183289

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	HDA more info	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 more info	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.