MRPL24

protein-coding

mitochondrial ribosomal protein L24, 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 which is more than twice the size of its E.coli counterpart (EcoL24). Sequence analysis identified two transcript variants that encode the same protein. [provided by RefSeq, Jul 2008]

MANE transcript

NM_145729.3

Inheritance

AR

ClinVar variants

U:40B:2

Top phenotype

MRPL24-related condition

gnomAD constraint

pLI —, LoF o/e 0.8

Max pathogenic AF

—

Genomic locus

chr1:156,737,303-156,741,590

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~4.3 kb
Loading mutation effect viewer...

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 *MRPL24* and primary mitochondrial disease was evaluated using the ClinGen Clinical Validity Framework as of January 27, 2025. The *MRPL24* gene encodes the mitochondrial ribosomal protein L24. The first and only report of the *MRPL24* gene in relation to autosomal recessive primary mitochondrial disease was in 2020 (PMID: 32344152), in a girl with cerebellar atrophy, choreoathetosis, intellectual disability and combined complex I and IV deficiency. 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 one homozygous missense variant identified in one case from one publication (PMID: 32344152). This girl had normal development until age 8 months when she experienced developmental regression (lost ability to sit and vocalize). By age 3 years, she had spasticity, dystonic posturing of distal upper and lower limbs, and dyskinetic facial grimacing. By age 8 years, she was sitting with support. She also had intellectual disability with lack of interaction with the environment and behavioral disturbance. Her course was stable at 14 years. Brain imaging at age three years showed bilateral alterations at the level of the putamen and cerebellar atrophy. She had elevated plasma lactate and decreased mitochondrial respiratory chain activities (combined defect of complexes I and IV) in skeletal muscle and cultured skin fibroblasts. 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) and a zebrafish model (PMID: 32344152). 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 MRPL24 variants in ClinVar

2 Conditions Cataloged
not specifiedTotal: 34
MRPL24-related conditionTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_145729.3. 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
1
clinvar
1
clinvar
2
missense
35
clinvar
1
clinvar
36
nonsense
0
start loss
0
frameshift
1
clinvar
1
splice donor/acceptor (+/-2bp)
3
clinvar
3
Total00402042
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 79 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_145729.3RefSeqNP_663781.15MANE Select
ENST00000361531.6EnsemblENSP00000354525.25MANE Select
NM_024540.4RefSeqNP_078816.25Standard
ENST00000368211.8EnsemblENSP00000357194.45Standard

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

  • mitochondrial translational elongation
  • mitochondrial translational termination

Molecular Function

  • 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
ENST00000361531
Coding exons
5
Length
4288
Individuals with no LoFs
125723
Homozygous LoFs
0
Heterozygous LoFs
25
Defined
125748
p
0.0000994
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.4251211350.8970.000008251381
Missense (PolyPhen)3136.2420.85536410
Synonymous0.9783947.60.8200.00000253436
Loss of Function0.6581012.50.7998.14e-7122

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000250.00025rare
Latino/Admixed American0.0000290.000029rare
Ashkenazi Jewish00.0absent
East Asian0.0000540.000054rare
Finnish00.0absent
European (Non-Finnish)0.000170.00017rare
South Asian00.0absent
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec
0.0867

Intolerance Scores

LoFtool
0.424
RVIS EVS
0.5
RVIS percentile EVS
79.89

Essentials

Essential (CRISPR)
E
Essential (CRISPR2)
S
Essential (gene trap)
E
Indispensability pred.
E
Indispensability score
0.948

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
For research and educational, non-commercial use only. Not for clinical or diagnostic use. GeneBe does not provide medical advice. Data use for AI modeling is prohibited: if used, the cost is $0.001 per byte of downloaded uncompressed data.