MRPL3
protein-codingmitochondrial ribosomal protein L3, the group of Small nucleolar RNA protein coding host genes|Large subunit mitochondrial ribosomal proteins|Mitochondrial ribosomal proteins
Gene summary
Mammalian mitochondrial ribosomal proteins are encoded by nuclear genes and help in protein synthesis within the mitochondrion. Mitochondrial ribosomes (mitoribosomes) consist of a small 28S subunit and a large 39S subunit. They have an estimated 75% protein to rRNA composition compared to prokaryotic ribosomes, where this ratio is reversed. Another difference between mammalian mitoribosomes and prokaryotic ribosomes is that the latter contain a 5S rRNA. Among different species, the proteins comprising the mitoribosome differ greatly in sequence, and sometimes in biochemical properties, which prevents easy recognition by sequence homology. This gene encodes a 39S subunit protein that belongs to the L3P ribosomal protein family. A pseudogene corresponding to this gene is found on chromosome 13q. [provided by RefSeq, Jul 2008]
- RPML3
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~40.8 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0044970
Submitter: ClinGen
The relationship between *MRPL3* and primary mitochondrial disease was evaluated using the ClinGen Clinical Validity Framework as of August 15, 2022. The *MRPL3* gene encodes the mitochondrial ribosomal protein L3, a large mitochondrial ribosomal subunit protein. The *MRPL3* gene was first reported in relation to autosomal recessive primary mitochondrial disease in 2011 (PMID: 21786366). While various names could be given to the constellation of features seen in those with *MRPL3*-related disease (including combined oxidative phosphorylation deficiency 9), pathogenic variants in this gene cause a primary mitochondrial disease. Therefore, the *MRPL3* phenotype has been lumped into one disease entity according to the ClinGen Lumping and Splitting Framework. Evidence supporting this gene-disease relationship includes case-level data and experimental data. This curation included four variants (one missense variant present in the compound heterozygous state in two probands, another missense variant present in the homozygous state in one proband, one frameshift, and one deletion) identified in three probands from three publications (PMID: 21786366, 27815843, 34008913). Age of onset in affected individuals ranged from the first day of life to six months old and outcomes ranged from death by 11 months old to alive at 11 years old. Features seen in affected individuals include severe infantile hypertrophic cardiomyopathy, hepatopathy, failure to thrive/feeding difficulty, and sensorineural hearing loss. Fibroblast testing showed a combined oxidative phosphorylation deficiency and a marked decrease of fully assembled complexes I, IV, and V, with normal complex II). Brain imaging was consistent with Leigh syndrome in one proband and an elevated lactate peak on brain MRS was seen in two probands. Laboratory abnormalities include hypoglycemia, elevated plasma alanine, and lactic acidosis. The mechanism of disease appears to be loss of function. This gene-disease relationship is also supported by a biochemical function (mitochondrial translation) shared with other genes associated with primary mitochondrial disease, functional alteration in patient cells, and model systems (PMIDs: 21786366, 32341096). In summary, there is moderate evidence to support this gene-disease relationship. While more evidence is needed to establish this relationship definitively, no convincing evidence has emerged that contradicts the gene-disease relationship. This classification was approved by the NICHD/NINDS U24 ClinGen Mitochondrial Disease Gene Curation Expert Panel on August 15, 2022 (SOP Version 9).
Inheritance Pattern: AR
Disease ID:MONDO:0013811
Submitter: Ambry Genetics
Inheritance Pattern: AR
Disease ID:MONDO:0013811
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0013811
Submitter: PanelApp Australia
Clinical Genomic Database (CGD)
Manifestation: Biochemical; Cardiovascular; Gastrointestinal; Musculoskeletal; Neurologic
Intervention: General
Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to MRPL3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_007208.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 3 | 18 | 3 | 24 | ||
| missense | 1 | 72 | 7 | 1 | 81 | |
| nonsense | 2 | 2 | ||||
| start loss | 0 | |||||
| frameshift | 1 | 2 | 1 | 4 | ||
| splice donor/acceptor (+/-2bp) | 1 | 1 | 6 | 8 | ||
| Total | 2 | 4 | 84 | 25 | 4 | 119 |
Highest pathogenic variant AF is 0.000030424277
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_009139.1 | 10 | MANE Select | |
| Ensembl | ENSP00000264995.2 | 10 | MANE Select | |
| Ensembl | ENSP00000398536.2 | 11 | Standard | |
| Ensembl | ENSP00000398536.2 | 11 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Ribosome - Homo sapiens (human)
- Mitochondrial translation initiation
- Translation
- Metabolism of proteins
- Mitochondrial translation elongation
Biological Process
- translation
- mitochondrial translational elongation
- mitochondrial translational termination
Molecular Function
- RNA binding
- structural constituent of ribosome
Cellular Component
- mitochondrion
- mitochondrial inner membrane
- mitochondrial large ribosomal subunit
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000264995
- Coding exons
- 10
- Length
- 40772
- Individuals with no LoFs
- 125693
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 55
- Defined
- 125748
- p
- 0.000219
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.160 | 200 | 194 | 1.03 | 0.00000973 | 2248 |
| Missense (PolyPhen) | 72 | 78.899 | 0.91256 | 947 | ||
| Synonymous | -0.963 | 82 | 71.6 | 1.14 | 0.00000385 | 671 |
| Loss of Function | 0.248 | 19 | 20.2 | 0.940 | 9.56e-7 | 239 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000063 | 0.000062 | rare |
| Latino/Admixed American | 0.00041 | 0.00040 | rare |
| Ashkenazi Jewish | 0.00030 | 0.00030 | rare |
| East Asian | 0.000055 | 0.000054 | rare |
| Finnish | 0.000093 | 0.000092 | rare |
| European (Non-Finnish) | 0.00025 | 0.00025 | rare |
| South Asian | 0.00017 | 0.00016 | rare |
| Other | 0.00021 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Disease
- DISEASE: Combined oxidative phosphorylation deficiency 9 (COXPD9) [MIM:614582]: A mitochondrial disease characterized by failure to thrive, poor feeding, hypertrophic cardiomyopathy, hepatomegaly, and psychomotor retardation. Death in infancy has been observed in some cases. {ECO:0000269|PubMed:21786366}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.131
Intolerance Scores
- LoFtool
- 0.889
- RVIS EVS
- -0.09
- RVIS percentile EVS
- 46.92
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- N
- Essential (gene trap)
- E
- Indispensability pred.
- E
- Indispensability score
- 0.815
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |