MRPS25
protein-codingmitochondrial ribosomal protein S25, the group of Small 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 28S subunit protein. A pseudogene corresponding to this gene is found on chromosome 4. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2016]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~55.7 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: Unknown
Disease ID:MONDO:0033570
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0004675
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0004675
Submitter: Franklin by Genoox
A subject with dyskinetic cerebral palsy and partial agenesis of the corpus callosum and some skeletal dysplasia. Using exome sequencing, we identified a homozygous variant c.215C>T in MRPS25
Inheritance Pattern: AR
Disease ID:MONDO:0044970
Submitter: ClinGen
The relationship between *MRPS25* and primary mitochondrial disease was evaluated using the ClinGen Clinical Validity Framework as of June 20, 2024. The *MRPS25* gene encodes the mitochondrial ribosomal protein S25, a component of the small subunit of the mitochondrial ribosome. The first and only report of *MRPS25* in relation to autosomal recessive primary mitochondrial disease was in 2019 (PMID: 31039582), in a 25-year-old man with a history of chorea, dystonia, partial agenesis of corpus callosum, adrenal insufficiency, short stature, and microcephaly. Muscle biopsy in childhood was originally unremarkable but repeat biopsy at 19 years old showed COX-negative fibers and reduced activities of the mitochondrial respiratory chain enzymes. He had a homozygous missense variant in *MRPS25*. While various names could be given to the constellation of features seen in those with *MRPS25*-related disorders, pathogenic variants in this gene cause a primary mitochondrial disease. Therefore, the MRPS25 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 the one missense variant noted above in one case in one publication (PMID: 31039582). The mechanism of disease is loss of function This gene-disease association is also supported by the known biochemical function of *MRPS25* in mitochondrial translation and rescue studies performed in patient cells (PMID: 31039582). 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 on June 20, 2024 (SOP Version 10).
Clinical Genomic Database (CGD)
Manifestation: Biochemical; Endocrine; Neurologic
Intervention: Endocrine
Rationale: In addition to other features, an individual has been described as involving adrenal insufficiency requiring hydrocortisone replacement, and awareness may allow early diagnosis and medical management
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to MRPS25 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_022497.5. 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 | 3 | ||||
| missense | 1 | 35 | 36 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 1 | 0 | 36 | 3 | 0 | 40 |
Highest pathogenic variant AF is 0.000007438963
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_071942.1 | 4 | MANE Select | |
| Ensembl | ENSP00000253686.2 | 4 | MANE Select | |
| Ensembl | ENSP00000396828.1 | 3 | Standard | |
| Ensembl | ENSP00000407733.2 | 3 | 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
Molecular Function
- structural constituent of ribosome
Cellular Component
- mitochondrion
- mitochondrial inner membrane
- ribosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000253686
- Coding exons
- 4
- Length
- 22876
- Individuals with no LoFs
- 125737
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 11
- Defined
- 125748
- p
- 0.0000437
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.809 | 73 | 95.2 | 0.767 | 0.00000478 | 1138 |
| Missense (PolyPhen) | 16 | 24.074 | 0.66462 | 287 | ||
| Synonymous | 0.207 | 36 | 37.6 | 0.957 | 0.00000198 | 308 |
| Loss of Function | 0.811 | 6 | 8.56 | 0.701 | 5.11e-7 | 94 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000032 | 0.000029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00011 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000063 | 0.000062 | rare |
| South Asian | 0.000065 | 0.000065 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
Recessive Scores
- pRec
- 0.0978
Intolerance Scores
- LoFtool
- 0.458
- RVIS EVS
- 0.13
- RVIS percentile EVS
- 62.74
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- E
- Essential (gene trap)
- E
- Indispensability pred.
- E
- Indispensability score
- 0.988
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |