MRPS25

protein-coding

mitochondrial 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

NM_022497.5

Inheritance

AR

ClinVar variants

P:1U:36B:3

Top phenotype

Combined oxidative phosphorylation deficiency 50

gnomAD constraint

pLI —, LoF o/e 0.7

Max pathogenic AF

—

Genomic locus

chr3:15,009,611-15,065,339

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~55.7 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

combined oxidative phosphorylation deficiency 50LIMITED

Inheritance Pattern: Unknown

Disease ID:MONDO:0033570

Submitter: Labcorp Genetics (formerly Invitae)

mitochondrial encephalomyopathyLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0004675

Submitter: PanelApp Australia

mitochondrial encephalomyopathyLIMITED

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

mitochondrial diseaseLIMITED

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)

Combined oxidative phosphorylation deficiency 50AR

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

Refs: 31039582Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to MRPS25 variants in ClinVar

3 Conditions Cataloged
not specifiedTotal: 31
not providedTotal: 4
Combined oxidative phosphorylation deficiency 50Total: 2

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.

EffectPLPVUSLBBSum
synonymous
3
clinvar
3
missense
1
clinvar
35
clinvar
36
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
1
clinvar
1
Total10363040

Highest pathogenic variant AF is 0.000007438963

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 56 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_022497.5RefSeqNP_071942.14MANE Select
ENST00000253686.7EnsemblENSP00000253686.24MANE Select
ENST00000420267.6EnsemblENSP00000396828.13Standard
ENST00000444840.6EnsemblENSP00000407733.23Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.8097395.20.7670.000004781138
Missense (PolyPhen)1624.0740.66462287
Synonymous0.2073637.60.9570.00000198308
Loss of Function0.81168.560.7015.11e-794

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American0.0000320.000029rare
Ashkenazi Jewish00.0absent
East Asian0.000110.000054rare
Finnish00.0absent
European (Non-Finnish)0.0000630.000062rare
South Asian0.0000650.000065rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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