MRPL3

protein-coding

mitochondrial 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]

Previous symbols:
  • RPML3

MANE transcript

NM_007208.4

Inheritance

AR

ClinVar variants

P:6U:84B:29

Top phenotype

Combined oxidative phosphorylation deficiency 9

gnomAD constraint

pLI —, LoF o/e 0.94

Max pathogenic AF

—

Genomic locus

chr3:131,462,212-131,502,983

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~40.8 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

mitochondrial diseaseMODERATE

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).

combined oxidative phosphorylation defect type 9LIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0013811

Submitter: Ambry Genetics

combined oxidative phosphorylation defect type 9STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0013811

Submitter: Labcorp Genetics (formerly Invitae)

combined oxidative phosphorylation defect type 9STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0013811

Submitter: PanelApp Australia

Clinical Genomic Database (CGD)

Combined oxidative phosphorylation deficiency 9AR

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

Refs: 21786366Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to MRPL3 variants in ClinVar

5 Conditions Cataloged
not providedTotal: 94
not specifiedTotal: 64
Combined oxidative phosphorylation defect type 9Total: 8
MRPL3-related disorderTotal: 5
Neonatal encephalopathyTotal: 1

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.

EffectPLPVUSLBBSum
synonymous
3
clinvar
18
clinvar
3
clinvar
24
missense
1
clinvar
72
clinvar
7
clinvar
1
clinvar
81
nonsense
2
clinvar
2
start loss
0
frameshift
1
clinvar
2
clinvar
1
clinvar
4
splice donor/acceptor (+/-2bp)
1
clinvar
1
clinvar
6
clinvar
8
Total2484254119

Highest pathogenic variant AF is 0.000030424277

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 37 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_007208.4RefSeqNP_009139.110MANE Select
ENST00000264995.8EnsemblENSP00000264995.210MANE Select
ENST00000425847.6EnsemblENSP00000398536.211Standard
ENST00000425847.7EnsemblENSP00000398536.211Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense-0.1602001941.030.000009732248
Missense (PolyPhen)7278.8990.91256947
Synonymous-0.9638271.61.140.00000385671
Loss of Function0.2481920.20.9409.56e-7239

Population LoF Frequency

PopulationCAFp-valueStatus
African0.0000630.000062rare
Latino/Admixed American0.000410.00040rare
Ashkenazi Jewish0.000300.00030rare
East Asian0.0000550.000054rare
Finnish0.0000930.000092rare
European (Non-Finnish)0.000250.00025rare
South Asian0.000170.00016rare
Other0.000210.00016rare

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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