PRORP

protein only RNase P catalytic subunit, the group of Pentatricopeptide repeat containing|Mitochondrial RNase P complex

Basic information

Region (hg38): 14:35121846-35277622

Previous symbols: [ "KIAA0391" ]

Links

ENSG00000100890 ∙ NCBI:9692 ∙ OMIM:609947 ∙ HGNC:19958 ∙ Uniprot:O15091 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• combined oxidative phosphorylation deficiency 54 (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Combined oxidative phosphorylation deficiency 54	AR	Audiologic/Otolaryngologic	Early recognition and treatment of hearing impairment may improve outcomes, including speech and language development	Audiologic/Otolaryngologic; Biochemical; Endocrine; Neurologic; Obstetric	34715011

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PRORP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRORP gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				3		3
missense			25	5	2	32
nonsense			1			1
start loss						0
frameshift			2			2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	28	9	2

Variants in PRORP

This is a list of pathogenic ClinVar variants found in the PRORP region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
14-35121922-G-A		not specified	Uncertain significance (Jul 19, 2023)
14-35121968-T-C		Gonadal dysgenesis, dysmorphic facies, retinal dystrophy, and myopathy • Spermatogenic failure 36 • PPP2R3C-related disorder	Benign (Oct 25, 2021)
14-35123256-ATTTG-A		not specified	Uncertain significance (May 04, 2022)
14-35123284-G-C		not specified	Uncertain significance (Feb 27, 2024)
14-35123346-C-A		not specified	Uncertain significance (Nov 09, 2021)
14-35123391-A-G		not specified	Uncertain significance (Dec 18, 2023)
14-35123396-A-G		not specified	Likely benign (Dec 17, 2023)
14-35123400-C-T		not specified	Uncertain significance (Aug 11, 2022)
14-35123406-A-G		not specified	Uncertain significance (Jan 23, 2024)
14-35123420-AC-A		Combined oxidative phosphorylation deficiency 54	Uncertain significance (Mar 29, 2024)
14-35123421-C-T		not specified	Likely benign (Nov 14, 2023)
14-35123429-A-G		not specified	Uncertain significance (May 08, 2024)
14-35123432-G-A		not specified	Uncertain significance (May 14, 2024)
14-35123465-A-G		not specified	Uncertain significance (Oct 24, 2024)
14-35123473-G-A			Likely benign (Dec 01, 2023)
14-35123474-C-A		not specified	Uncertain significance (Mar 16, 2022)
14-35123495-T-G		not specified	Uncertain significance (Jun 28, 2022)
14-35123511-C-G		not specified	Uncertain significance (Mar 08, 2024)
14-35123523-G-A		not specified	Uncertain significance (Jul 30, 2024)
14-35123523-G-C		not specified	Uncertain significance (Aug 28, 2024)
14-35123556-C-T		not specified	Uncertain significance (Dec 21, 2023)
14-35123636-T-G		not specified	Uncertain significance (Mar 15, 2024)
14-35123671-T-G		not specified	Likely benign (Jun 12, 2023)
14-35123682-C-T		not specified	Uncertain significance (Jan 25, 2023)
14-35123717-G-A		not specified	Uncertain significance (Oct 29, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRORP	protein_coding	protein_coding	ENST00000534898	7	152220

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.33e-13	0.0902	125698	0	49	125747	0.000195

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.777	270	308	0.875	0.0000157	3843
Missense in Polyphen		155	189.56	0.81768		2519
Synonymous	0.793	101	112	0.905	0.00000544	1099
Loss of Function	0.678	22	25.7	0.856	0.00000125	324

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000235	0.000235
Ashkenazi Jewish	0.00	0.00
East Asian	0.000219	0.000217
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000278	0.000273
Middle Eastern	0.000219	0.000217
South Asian	0.000131	0.000131
Other	0.000331	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalytic ribonuclease component of mitochondrial ribonuclease P, a complex composed of TRMT10C/MRPP1, HSD17B10/MRPP2 and MRPP3, which cleaves tRNA molecules in their 5'-ends (PubMed:18984158, PubMed:25953853). The presence of TRMT10C/MRPP1, HSD17B10/MRPP2 is required to catalyze tRNA molecules in their 5'-ends (PubMed:25953853). {ECO:0000269|PubMed:18984158, ECO:0000269|PubMed:25953853}.
• Pathway: tRNA processing;tRNA modification in the mitochondrion;Metabolism of RNA (Consensus)

Recessive Scores

• pRec: 0.0833

Intolerance Scores

• loftool: 0.927
• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.74

Haploinsufficiency Scores

• pHI: 0.0313
• hipred: N
• hipred_score: 0.146
• ghis: 0.385

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.726

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: 1110008L16Rik

Gene ontology

• Biological process: tRNA 5'-leader removal;RNA phosphodiester bond hydrolysis, endonucleolytic;mitochondrial tRNA processing;mitochondrial tRNA 5'-end processing
• Cellular component: nucleus;mitochondrion;mitochondrial matrix;mitochondrial ribonuclease P complex;mitochondrial nucleoid
• Molecular function: ribonuclease P activity;metal ion binding