MRPL38

protein-coding

mitochondrial 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

NM_032478.4

Inheritance

AR

ClinVar variants

U:85B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.72

Max pathogenic AF

—

Genomic locus

chr17:75,898,644-75,905,093

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~6.4 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

mitochondrial diseaseLIMITED

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

2 Conditions Cataloged
not specifiedTotal: 81
not providedTotal: 1

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.

EffectPLPVUSLBBSum
synonymous
2
clinvar
2
clinvar
4
missense
82
clinvar
2
clinvar
84
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
1
clinvar
1
Total00854089
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 36 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_032478.4RefSeqNP_115867.29MANE Select
ENST00000309352.4EnsemblENSP00000308275.49MANE Select
ENST00000884825.1EnsemblENSP00000554885.19Standard
ENST00000884827.1EnsemblENSP00000554886.19Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.1922222300.9640.00001472391
Missense (PolyPhen)8489.7210.93624940
Synonymous-0.77110393.51.100.00000562760
Loss of Function1.201622.10.7240.00000121229

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American0.000120.00012rare
Ashkenazi Jewish00.0absent
East Asian0.000330.00033rare
Finnish0.000130.000092rare
European (Non-Finnish)0.000310.00030rare
South Asian0.0000670.000065rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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