MRPL38
protein-codingmitochondrial ribosomal protein L38, the group of 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. [provided by RefSeq, Jul 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~6.4 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0044970
Submitter: ClinGen
The relationship between *MRPL38* and primary mitochondrial disease was evaluated using the ClinGen Clinical Validity Framework as of January 27, 2025. The *MRPL38* gene encodes the mitochondrial ribosomal protein L38. The first and only report of the *MRPL38* gene in relation to autosomal recessive primary mitochondrial disease was in 2022 (PMID: 35379322) in a girl with Leigh syndrome spectrum disorder. This is one disease entity according to the ClinGen Lumping and Splitting Framework, and is considered a primary mitochondrial disease. Evidence supporting this gene-disease relationship includes case-level data and experimental data. This curation included two variants identified (one missense, one deletion) in one case from one publication (PMID: 35379322). This girl had Leigh syndrome spectrum disorder based on basal ganglia changes on brain imaging and neurodevelopmental delay, and also had intellectual disability, seizures, encephalopathy, and complex I and IV defects. The mechanism of disease is loss of function. This gene-disease relationship is also supported by a biochemical function shared with other genes associated with primary mitochondrial disease (PMID: 33340416). Additional functional evidence is provided in a pre-print (DOI:10.1101/2021.03.09.21253187) however this work has not yet been published. In summary, there is limited 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 January 27, 2025 (SOP Version 11).
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to MRPL38 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_032478.4. 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 | 2 | 2 | 4 | |||
| missense | 82 | 2 | 84 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 85 | 4 | 0 | 89 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_115867.2 | 9 | MANE Select | |
| Ensembl | ENSP00000308275.4 | 9 | MANE Select | |
| Ensembl | ENSP00000554885.1 | 9 | Standard | |
| Ensembl | ENSP00000554886.1 | 9 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Mitochondrial translation initiation
- Translation
- Metabolism of proteins
- Mitochondrial translation elongation
- Mitochondrial translation termination
Biological Process
- mitochondrial translational elongation
- mitochondrial translational termination
Cellular Component
- mitochondrion
- mitochondrial inner membrane
- mitochondrial large ribosomal subunit
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000309352
- Coding exons
- 9
- Length
- 11176
- Individuals with no LoFs
- 125456
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 48
- Defined
- 125504
- p
- 0.000191
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.192 | 222 | 230 | 0.964 | 0.0000147 | 2391 |
| Missense (PolyPhen) | 84 | 89.721 | 0.93624 | 940 | ||
| Synonymous | -0.771 | 103 | 93.5 | 1.10 | 0.00000562 | 760 |
| Loss of Function | 1.20 | 16 | 22.1 | 0.724 | 0.00000121 | 229 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.00012 | 0.00012 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00033 | 0.00033 | rare |
| Finnish | 0.00013 | 0.000092 | rare |
| European (Non-Finnish) | 0.00031 | 0.00030 | rare |
| South Asian | 0.000067 | 0.000065 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
Intolerance Scores
- LoFtool
- 0.654
- RVIS EVS
- 0.02
- RVIS percentile EVS
- 55.69
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- E
- Essential (gene trap)
- E
- Indispensability pred.
- E
- Indispensability score
- 0.871
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |