MRPS22
protein-codingmitochondrial ribosomal protein S22, 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 that does not seem to have a counterpart in prokaryotic and fungal-mitochondrial ribosomes. This gene lies telomeric of and is transcribed in the opposite direction from the forkhead box L2 gene. A pseudogene corresponding to this gene is found on chromosome Xq. [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 ~354.7 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0012718
Submitter: PanelApp Australia
Inheritance Pattern: AD
Disease ID:MONDO:0009299
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0012718
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0044970
Submitter: ClinGen
The relationship between *MRPS22* and primary mitochondrial disease was evaluated using the ClinGen Clinical Validity Framework as of July 18, 2022. The *MRPS22* gene encodes the mitochondrial ribosomal protein S22, a component of the small subunit of the mitochondrial ribosome. *MRPS22* was first reported in relation to autosomal recessive mitochondrial disease in 2007 (PMID: 17873122). While various names have been given to the constellation of features seen in those with *MRPS22*-related disease, pathogenic variants in this gene cause a primary mitochondrial disease. Therefore, the *MRPS22* 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 five unique variants: four missense variants and one frameshift variant from five probands across four publications. Familial segregation data were also included in scoring (PMIDs: 17873122, PMID:29566152). The condition was first described in two sisters with severe lactic acidosis, hypotonia, ascites, hyperammonemia, and hypertrophic cardiomyopathy. Both sisters died within the first month of life. Muscle biopsy respiratory chain activities were consistent with a mitochondrial translation defect (PMID: 17873122). Subsequent publications have shown there are two phenotypes caused by *MRPS22* pathogenic variants. The first is a neonatal profound lactic acidosis with multi-organ failure that is often fatal (PMIDs: 25663021, 21189481). The second phenotype involves premature ovarian insufficiency with or without peripheral neuropathy (PMID: 29566152). Given the association of premature ovarian insufficiency with other mitochondrial disorders of translation, such as deficiencies of the HARS2 and LARS2 mitochondrial tRNA aminoacyl synthetases, all cases were scored for this curation. Of note, a Turkish proband with mosaic Down syndrome and Leigh syndrome has been reported but was not considered in this curation, given a lack of functional evidence and the presence of other potential candidate variants (PMID: 28752220). This gene-disease association is also supported by known protein interaction with other proteins involved in mitochondrial translation, documented respiratory chain deficiencies and assembly defects in patient cell lines, and mouse and drosophila models which showed embryonic lethality or sterility (PMIDs: 17873122, 18539099, 21189481, 29566152). In summary, there is definitive evidence to support this gene-disease relationship. This curation reached a score of 11.7 which is between moderate and definitive, and the Mitochondrial Disease Gene Curation Expert Panel opted to score as definitive. This has been repeatedly demonstrated and has been upheld over time. 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 July 18, 2022 (SOP Version 9).
Inheritance Pattern: AR
Disease ID:MONDO:0012718
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0020857
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0012718
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0020857
Submitter: Labcorp Genetics (formerly Invitae)
Clinical Genomic Database (CGD)
Manifestation: Biochemical; Cardiovascular; Craniofacial; Endocrine; Obstetric; Renal; Musculoskeletal; Neurologic
Intervention: General
Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to MRPS22 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_020191.4. 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 | 5 | 29 | 34 | |||
| missense | 1 | 3 | 97 | 8 | 1 | 110 |
| nonsense | 4 | 3 | 1 | 8 | ||
| start loss | 0 | |||||
| frameshift | 5 | 5 | 3 | 13 | ||
| splice donor/acceptor (+/-2bp) | 2 | 1 | 2 | 5 | ||
| Total | 12 | 12 | 108 | 37 | 1 | 170 |
Highest pathogenic variant AF is 0.00014498716
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_064576.1 | 8 | MANE Select | |
| Ensembl | ENSP00000505414.1 | 8 | MANE Select | |
| RefSeq | NP_001350786.1 | 8 | Standard | |
| RefSeq | NP_001350822.1 | 8 | 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
- biological_process
- mitochondrial translational elongation
- mitochondrial translational termination
Molecular Function
- structural constituent of ribosome
Cellular Component
- mitochondrion
- mitochondrial inner membrane
- mitochondrial ribosome
- mitochondrial small ribosomal subunit
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000495075
- Coding exons
- 8
- Length
- 351418
- Individuals with no LoFs
- 125700
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 48
- Defined
- 125748
- p
- 0.000191
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.131 | 198 | 203 | 0.974 | 0.0000110 | 2348 |
| Missense (PolyPhen) | 63 | 74.494 | 0.8457 | 849 | ||
| Synonymous | -1.44 | 86 | 70.6 | 1.22 | 0.00000350 | 691 |
| Loss of Function | 1.93 | 11 | 20.4 | 0.539 | 0.00000114 | 229 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00043 | 0.00043 | rare |
| Latino/Admixed American | 0.00012 | 0.00012 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.00027 | 0.00027 | rare |
| South Asian | 0.000065 | 0.000065 | rare |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Disease
- DISEASE: Combined oxidative phosphorylation deficiency 5 (COXPD5) [MIM:611719]: A mitochondrial disease resulting in severe metabolic acidosis, edema, hypertrophic cardiomyopathy, tubulopathy, and hypotonia. {ECO:0000269|PubMed:17873122}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.204
Intolerance Scores
- LoFtool
- 0.343
- RVIS EVS
- 0.44
- RVIS percentile EVS
- 77.7
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- E
- Indispensability pred.
- N
- Indispensability score
- 0.0106
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |