MRPS22

protein-coding

mitochondrial 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

NM_020191.4

Inheritance

AR, AD

ClinVar variants

P:24U:108B:38

Top phenotype

Combined oxidative phosphorylation deficiency 5; Ovarian dysgenesis 7

gnomAD constraint

pLI —, LoF o/e 0.54

Max pathogenic AF

—

Genomic locus

chr3:139,005,806-139,360,497

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~354.7 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

hypotonia with lactic acidemia and hyperammonemiaSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0012718

Submitter: PanelApp Australia

46 XX gonadal dysgenesisSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0009299

Submitter: Orphanet

hypotonia with lactic acidemia and hyperammonemiaSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0012718

Submitter: Orphanet

mitochondrial diseaseDEFINITIVE

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).

hypotonia with lactic acidemia and hyperammonemiaSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0012718

Submitter: Labcorp Genetics (formerly Invitae)

ovarian dysgenesis 7STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0020857

Submitter: PanelApp Australia

hypotonia with lactic acidemia and hyperammonemiaSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0012718

Submitter: G2P

ovarian dysgenesis 7LIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0020857

Submitter: Labcorp Genetics (formerly Invitae)

Clinical Genomic Database (CGD)

Combined oxidative phosphorylation deficiency 5; Ovarian dysgenesis 7AR

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

Refs: 17873122; 21189481; 29566152Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to MRPS22 variants in ClinVar

12 Conditions Cataloged
not providedTotal: 137
Inborn genetic diseasesTotal: 65
Hypotonia with lactic acidemia and hyperammonemiaTotal: 38
not specifiedTotal: 22
MRPS22-related disorderTotal: 17
Ovarian dysgenesis 7Total: 8
46 XX gonadal dysgenesisTotal: 2
MRPS22-related disordersTotal: 2

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.

EffectPLPVUSLBBSum
synonymous
5
clinvar
29
clinvar
34
missense
1
clinvar
3
clinvar
97
clinvar
8
clinvar
1
clinvar
110
nonsense
4
clinvar
3
clinvar
1
clinvar
8
start loss
0
frameshift
5
clinvar
5
clinvar
3
clinvar
13
splice donor/acceptor (+/-2bp)
2
clinvar
1
clinvar
2
clinvar
5
Total1212108371170

Highest pathogenic variant AF is 0.00014498716

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 43 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_020191.4RefSeqNP_064576.18MANE Select
ENST00000680020.1EnsemblENSP00000505414.18MANE Select
NM_001363857.1RefSeqNP_001350786.18Standard
NM_001363893.1RefSeqNP_001350822.18Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.1311982030.9740.00001102348
Missense (PolyPhen)6374.4940.8457849
Synonymous-1.448670.61.220.00000350691
Loss of Function1.931120.40.5390.00000114229

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000430.00043rare
Latino/Admixed American0.000120.00012rare
Ashkenazi Jewish00.0absent
East Asian0.000110.00011rare
Finnish0.0000460.000046rare
European (Non-Finnish)0.000270.00027rare
South Asian0.0000650.000065rare
Other0.000160.00016rare

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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