Gene Gene information from NCBI Gene database.
Entrez ID 55037
Gene name Pentatricopeptide repeat domain 3
Gene symbol PTCD3
Synonyms (NCBI Gene)
COXPD51MRP-S39mS39
Chromosome 2
Chromosome location 2p11.2
miRNA miRNA information provided by mirtarbase database.
670
miRTarBase ID miRNA Experiments Reference
MIRT005269 hsa-miR-16-5p pSILAC 18668040
MIRT028845 hsa-miR-26b-5p Microarray 19088304
MIRT005269 hsa-miR-16-5p Proteomics;Other 18668040
MIRT047373 hsa-miR-34a-5p CLASH 23622248
MIRT044063 hsa-miR-361-5p CLASH 23622248
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
28
GO ID Ontology Definition Evidence Reference
GO:0003723 Function RNA binding HDA 22658674, 22681889
GO:0003723 Function RNA binding IEA
GO:0005515 Function Protein binding IPI 19427859, 21516116, 24965446, 29892012, 31515488, 33961781
GO:0005654 Component Nucleoplasm IDA
GO:0005739 Component Mitochondrion HTP 34800366
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
614918 24717 ENSG00000132300
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
Q96EY7
Protein name Small ribosomal subunit protein mS39 (28S ribosomal protein S39, mitochondrial) (MRP-S39) (Pentatricopeptide repeat domain-containing protein 3, mitochondrial) (Transformation-related gene 15 protein) (TRG-15)
Protein function Mitochondrial RNA-binding protein that has a role in mitochondrial translation.
PDB 3J9M , 6NU2 , 6NU3 , 6RW4 , 6RW5 , 6VLZ , 6VMI , 6ZM5 , 6ZM6 , 6ZS9 , 6ZSA , 6ZSB , 6ZSC , 6ZSD , 6ZSE , 6ZSG , 7A5F , 7A5G , 7A5I , 7A5K , 7L08 , 7OG4 , 7P2E , 7PNX , 7PNY , 7PNZ , 7PO0 , 7PO1 , 7PO2 , 7PO3 , 7QI4 , 7QI5 , 7QI6 , 8ANY , 8CSP , 8CSQ , 8CSR , 8CSS , 8CST , 8CSU , 8K2A , 8OIR , 8OIS , 8QRK , 8QRL , 8QRM , 8QRN , 8RRI , 8XT0 , 8XT2
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF13041 PPR_2 254 303 PPR repeat family Repeat
PF13812 PPR_3 345 384 Pentatricopeptide repeat domain Repeat
Tissue specificity TISSUE SPECIFICITY: Abundant in testes, skeletal muscle and heart tissue. {ECO:0000269|PubMed:19427859}.
Sequence
MAVVSAVRWLGLRSRLGQPLTGRRAGLCEQARSCRFYSGSATLSKVEGTDVTGIEEVVIP
KKKTWDKVAVLQALASTVNRDTTAVPYVFQDDPYLMPASSLESRSFLLAKKSGENVAKFI
INSYPKYFQKDIAEPHIPCLMPEYFEPQIKDISEAALKERIELRKVKASVDMFDQLLQAG
TTVSLETTNSLLDLLCYYGDQEPSTDYHFQQTGQSEALEEENDETSRRKAGHQFGVTWRA
KNNAERIFSLMPEKNEHSYCTMIRGMVKHRAYEQALNLYTELLNNRLHADVYTFNALIEA
TVC
AINEKFEEKWSKILELLRHMVAQKVKPNLQTFNTILKCLRRFHVFARSPALQVLREM
KAIGIEPSLATYHHIIRLFDQPGD
PLKRSSFIIYDIMNELMGKRFSPKDPDDDKFFQSAM
SICSSLRDLELAYQVHGLLKTGDNWKFIGPDQHRNFYYSKFFDLICLMEQIDVTLKWYED
LIPSAYFPHSQTMIHLLQALDVANRLEVIPKIWKDSKEYGHTFRSDLREEILMLMARDKH
PPELQVAFADCAADIKSAYESQPIRQTAQDWPATSLNCIAILFLRAGRTQEAWKMLGLFR
KHNKIPRSELLNELMDSAKVSNSPSQAIEVVELASAFSLPICEGLTQRVMSDFAINQEQK
EALSNLTALTSDSDTDSSSDSDSDTSEGK
Sequence length 689
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  Reactome
    Mitochondrial translation elongation
Mitochondrial translation termination
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
5
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Combined oxidative phosphorylation deficiency 51 Likely pathogenic; Pathogenic rs1674335308, rs373659799, rs2466560501, rs2466586448, rs746897836, rs1301547272, rs1573859565 RCV003448988
RCV003448951
RCV003448953
RCV003990610
RCV004555086
View all (2 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
PTCD3-related disorder Likely pathogenic rs776660221 RCV003412097
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
Chronic lymphocytic leukemia/small lymphocytic lymphoma Uncertain significance ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
LEIGH SYNDROME ClinGen, GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus Likely benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
B-Cell Lymphomas B-Cell Lymphoma BEFREE 27635472
★☆☆☆☆
Found in Text Mining only
Glycogen Storage Disease Type IV Glycogen storage disease Pubtator 19427859 Associate
★☆☆☆☆
Found in Text Mining only
Leigh Disease Leigh Syndrome CLINGEN_DG 19427859, 25613900, 30607703
★☆☆☆☆
Found in Text Mining only
Leigh Disease Leigh Syndrome BEFREE 30607703
★☆☆☆☆
Found in Text Mining only
Leigh Disease Leigh syndrome Pubtator 36450274 Associate
★☆☆☆☆
Found in Text Mining only
LEIGH SYNDROME DUE TO MITOCHONDRIAL COMPLEX I DEFICIENCY Leigh Syndrome CLINGEN_DG 19427859, 25613900, 30607703
★☆☆☆☆
Found in Text Mining only
Leigh Syndrome Due To Mitochondrial Complex II Deficiency Leigh Syndrome CLINGEN_DG 19427859, 25613900, 30607703
★☆☆☆☆
Found in Text Mining only
Leigh Syndrome due to Mitochondrial Complex III Deficiency Leigh Syndrome CLINGEN_DG 19427859, 25613900, 30607703
★☆☆☆☆
Found in Text Mining only
Leigh Syndrome due to Mitochondrial Complex IV Deficiency Leigh Syndrome CLINGEN_DG 19427859, 25613900, 30607703
★☆☆☆☆
Found in Text Mining only
Leigh Syndrome due to Mitochondrial Complex V Deficiency Leigh Syndrome CLINGEN_DG 19427859, 25613900, 30607703
★☆☆☆☆
Found in Text Mining only