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PRORP protein only RNase P catalytic subunit [ Homo sapiens (human) ]

Gene ID: 9692, updated on 10-Mar-2024

Summary

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Official Symbol
PRORPprovided by HGNC
Official Full Name
protein only RNase P catalytic subunitprovided by HGNC
Primary source
HGNC:HGNC:19958
See related
Ensembl:ENSG00000100890 MIM:609947; AllianceGenome:HGNC:19958
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
MRPP3; COXPD54; KIAA0391
Summary
Enables ribonuclease P activity. Involved in mitochondrial tRNA 5'-end processing. Located in mitochondrion and nucleoplasm. Part of mitochondrial ribonuclease P complex. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in testis (RPKM 10.2), kidney (RPKM 8.4) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
14q13.2
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (35121839..35277622)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (29318793..29465226)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (35591758..35746828)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:35451517-35452218 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8259 Neighboring gene signal recognition particle 54 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8260 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5673 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8261 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8262 Neighboring gene family with sequence similarity 177 member A1 Neighboring gene uncharacterized LOC101927178 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:35571935-35572102 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr14:35581755-35582536 Neighboring gene protein phosphatase 2 regulatory subunit B''gamma Neighboring gene MED14-independent group 3 enhancer GRCh37_chr14:35590400-35591599 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:35591739-35592658 Neighboring gene PRORP-PSMA6 readthrough Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:35622091-35622592 Neighboring gene Sharpr-MPRA regulatory region 10139 Neighboring gene ribosomal protein L23a pseudogene 70 Neighboring gene septin 7 pseudogene 1 Neighboring gene mitochondrial ribosomal protein L57 pseudogene 8 Neighboring gene divergent-paired related homeobox pseudogene 3 Neighboring gene ribosomal protein L7a pseudogene 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8266 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8267 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8268 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:35761289-35761875 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8271 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8272 Neighboring gene ribosomal protein L9 pseudogene 3 Neighboring gene proteasome 20S subunit alpha 6 Neighboring gene Sharpr-MPRA regulatory region 8744 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:35801329-35802250 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr14:35802261-35802870 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:35805755-35806276 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8273 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:35811147-35812003 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:35816286-35816830 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8274 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8275 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:35836533-35837122 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:35837123-35837710 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:35837711-35838299 Neighboring gene CRISPRi-validated cis-regulatory element chr14.550 Neighboring gene Sharpr-MPRA regulatory region 4470 Neighboring gene PSMA6-RPLP0P3 intergenic CAGE-defined low expression enhancer Neighboring gene ribosomal protein lateral stalk subunit P0 pseudogene 3

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Bi-allelic variants in the mitochondrial RNase P subunit PRORP cause mitochondrial tRNA processing defects and pleiotropic multisystem presentations. Hochberg I, et al. Am J Hum Genet, 2021 Nov 4. PMID 34715011, Free PMC Article
  2. High-resolution genomic analysis of human mitochondrial RNA sequence variation. Hodgkinson A, et al. Science, 2014 Apr 25. PMID 24763589
  3. Structure of the nuclease subunit of human mitochondrial RNase P. Reinhard L, et al. Nucleic Acids Res, 2015 Jun 23. PMID 25953853, Free PMC Article
  4. Haplotypes encompassing the KIAA0391 and PSMA6 gene cluster confer a genetic link for myocardial infarction and coronary artery disease. Alsmadi O, et al. Ann Hum Genet, 2009 Sep. PMID 19624571
  5. Structural basis of RNA processing by human mitochondrial RNase P. Bhatta A, et al. Nat Struct Mol Biol, 2021 Sep. PMID 34489609, Free PMC Article

See all (47) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Comprehensive functional interrogation of susceptibility loci in GWASs identified KIAA0391 as a novel oncogenic driver via regulating pyroptosis in NSCLC.
    Title: Comprehensive functional interrogation of susceptibility loci in GWASs identified KIAA0391 as a novel oncogenic driver via regulating pyroptosis in NSCLC.
  2. Novel homozygous variants in PRORP expand the genotypic spectrum of combined oxidative phosphorylation deficiency 54.
    Title: Novel homozygous variants in PRORP expand the genotypic spectrum of combined oxidative phosphorylation deficiency 54.
  3. Bi-allelic variants in the mitochondrial RNase P subunit PRORP cause mitochondrial tRNA processing defects and pleiotropic multisystem presentations.
    Title: Bi-allelic variants in the mitochondrial RNase P subunit PRORP cause mitochondrial tRNA processing defects and pleiotropic multisystem presentations.
  4. Structural basis of RNA processing by human mitochondrial RNase P.
    Title: Structural basis of RNA processing by human mitochondrial RNase P.
  5. This study proposes low-resolution models of the MRPP1-MRPP2 and MRPP1-MRPP2-MRPP3 complexes that suggest the overall architecture, stoichiometry, and orientation of subunits and tRNA substrates.
    Title: Structural insight into the human mitochondrial tRNA purine N1-methyltransferase and ribonuclease P complexes.
  6. This study presents the crystal structure of human MRPP3, which features a remarkably distorted and hence non-productive active site that authors propose will switch to a fully productive state only upon association with MRPP1, MRPP2 and pre-tRNA substrate.
    Title: Structure of the nuclease subunit of human mitochondrial RNase P.
  7. using a genome-wide association study, found that posttranscriptional modification of functionally important sites in mitochondrial transfer RNAs (tRNAs) is under strong genetic control, largely driven by a missense mutation in MRPP3
    Title: High-resolution genomic analysis of human mitochondrial RNA sequence variation.
  8. Inhibition of mitochondrial RNase P by beta-amyloid is an unspecific effect and is not mediated by beta-amyloid interaction with SDR5C1.
    Title: The amyloid-β-SDR5C1(ABAD) interaction does not mediate a specific inhibition of mitochondrial RNase P.
  9. Haplotypes in KIAA0391 and PSMA6 genes is a genetic link for myocardial infarction and coronary artery disease.
    Title: Haplotypes encompassing the KIAA0391 and PSMA6 gene cluster confer a genetic link for myocardial infarction and coronary artery disease.
  10. Observational study of gene-disease association. (HuGE Navigator)
    Title: Haplotypes encompassing the KIAA0391 and PSMA6 gene cluster confer a genetic link for myocardial infarction and coronary artery disease.
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 54
MedGen: C5676912 OMIM: 619737 GeneReviews: Not available
not available

EBI GWAS Catalog

Description
Genome-wide association analysis identifies three psoriasis susceptibility loci.
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)

Genotypes

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

Readthrough PRORP-PSMA6

Readthrough gene: PRORP-PSMA6, Included gene: PSMA6

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables ribonuclease P activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables ribonuclease P activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in mitochondrial tRNA 5'-end processing IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in mitochondrial tRNA 5'-end processing IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in tRNA 5'-leader removal IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in mitochondrial matrix TAS
Traceable Author Statement
more info
  
located_in mitochondrial nucleoid IEA
Inferred from Electronic Annotation
more info
  
part_of mitochondrial ribonuclease P complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of mitochondrial ribonuclease P complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of mitochondrial ribonuclease P complex IPI
Inferred from Physical Interaction
more info
 PubMed 
part_of mitochondrial ribonuclease P complex TAS
Traceable Author Statement
more info
 PubMed 
located_in mitochondrion IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  

General protein information

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Preferred Names
mitochondrial ribonuclease P catalytic subunit
Names
mitochondrial RNase P protein 3
mitochondrial RNase P subunit 3
mitochondrial ribonuclease P protein 3
proteinaceous RNase P
NP_001243607.1
NP_001243608.1
NP_001243609.1
NP_001243610.1
NP_001401432.1
NP_055487.2

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_001256678.2 → NP_001243607.1  mitochondrial ribonuclease P catalytic subunit isoform 2

    See identical proteins and their annotated locations for NP_001243607.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an exon in the coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AB002389, AK304066, AL121594, DA459368
    Consensus CDS
    CCDS58312.1
    UniProtKB/Swiss-Prot
    O15091
    Related
    ENSP00000250377.8, ENST00000250377.11
    Conserved Domains (2) summary
    sd00004
    Location:174 → 204
    PPR; PPR repeat [structural motif]
    pfam16953
    Location:328 → 562
    PRORP; Protein-only RNase P

  2. NM_001256679.2 → NP_001243608.1  mitochondrial ribonuclease P catalytic subunit isoform 3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at a downstream, in-frame start codon, compared to variant 1. The encoded isoform (3) has a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AI431599, AK301931, AL121594, BP373829
    Consensus CDS
    CCDS58313.1
    UniProtKB/Swiss-Prot
    O15091
    Related
    ENSP00000474620.1, ENST00000604948.5
    Conserved Domains (2) summary
    sd00004
    Location:79 → 109
    PPR; PPR repeat [structural motif]
    pfam16953
    Location:247 → 483
    PRORP; Protein-only RNase P

  3. NM_001256680.2 → NP_001243609.1  mitochondrial ribonuclease P catalytic subunit isoform 4

    See identical proteins and their annotated locations for NP_001243609.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at a downstream, in-frame start codon, compared to variant 1. Variants 4 and 5 encode the same isoform (4), which has a shorter N-terminus compared to isoform 1.
    Source sequence(s)
    AA838769, AL121594, BX161487, DC404874
    Consensus CDS
    CCDS58314.1
    UniProtKB/TrEMBL
    A0A0A0MTQ0
    Related
    ENSP00000474299.1, ENST00000605870.5
    Conserved Domains (1) summary
    pfam16953
    Location:1 → 206
    PRORP; Protein-only RNase P

  4. NM_001256681.2 → NP_001243610.1  mitochondrial ribonuclease P catalytic subunit isoform 4

    See identical proteins and their annotated locations for NP_001243610.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at a downstream, in-frame start codon, compared to variant 1. Variants 4 and 5 encode the same isoform (4), which has a shorter N-terminus compared to isoform 1.
    Source sequence(s)
    AI431599, AL121594, BQ063741, DC404874, DT217089
    Consensus CDS
    CCDS58314.1
    UniProtKB/TrEMBL
    A0A0A0MTQ0
    Related
    ENSP00000324697.9, ENST00000321130.14
    Conserved Domains (1) summary
    pfam16953
    Location:1 → 206
    PRORP; Protein-only RNase P

  5. NM_001414503.1 → NP_001401432.1  mitochondrial ribonuclease P catalytic subunit isoform 1 precursor

    Status: VALIDATED

    Source sequence(s)
    AL121594
    UniProtKB/Swiss-Prot
    B4DXD9, B4E0S8, B4E211, C4AM93, D3DS99, D3DSA1, O15091, Q86SZ4, Q86YB5, Q8N5L5

  6. NM_014672.4 → NP_055487.2  mitochondrial ribonuclease P catalytic subunit isoform 1 precursor

    See identical proteins and their annotated locations for NP_055487.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1). Variants 1 and 6 both encode the same isoform (1).
    Source sequence(s)
    AA838769, AL121594, BX161394, DA459368
    Consensus CDS
    CCDS32063.1
    UniProtKB/Swiss-Prot
    B4DXD9, B4E0S8, B4E211, C4AM93, D3DS99, D3DSA1, O15091, Q86SZ4, Q86YB5, Q8N5L5
    Related
    ENSP00000440915.2, ENST00000534898.9
    Conserved Domains (2) summary
    sd00004
    Location:174 → 204
    PPR; PPR repeat [structural motif]
    pfam16953
    Location:342 → 578
    PRORP; Protein-only RNase P

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    35121839..35277622
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    29318793..29465226
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O15091.2 GenPept UniProtKB/Swiss-Prot:O15091

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