MRPS2
Basic information
Region (hg38): 9:135499984-135504673
Links
Phenotypes
GenCC
Source:
- combined oxidative phosphorylation deficiency 36 (Limited), mode of inheritance: AR
- combined oxidative phosphorylation deficiency 36 (Limited), mode of inheritance: Unknown
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Combined oxidative phosphorylation deficiency 36 | AR | General | 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 | Audiologic/Otolaryngologic; Biochemical; Neurologic | 29576219 |
ClinVar
This is a list of variants' phenotypes submitted to
- Combined oxidative phosphorylation deficiency 36 (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the MRPS2 gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
---|---|---|---|---|---|---|
synonymous | 15 | 16 | ||||
missense | 42 | 52 | ||||
nonsense | 1 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 1 | |||||
splice region | 1 | 3 | 4 | |||
non coding | 6 | |||||
Total | 1 | 1 | 45 | 21 | 8 |
Highest pathogenic variant AF is 0.0000131
Variants in MRPS2
This is a list of pathogenic ClinVar variants found in the MRPS2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
9-135500724-C-T | Combined oxidative phosphorylation deficiency 36 | Uncertain significance (Aug 14, 2023) | ||
9-135500735-C-A | not specified | Uncertain significance (Aug 02, 2021) | ||
9-135500735-C-T | not specified | Uncertain significance (Jul 21, 2024) | ||
9-135500741-A-G | not specified | Uncertain significance (Apr 12, 2024) | ||
9-135500755-TGAGC-T | Uncertain significance (Dec 11, 2023) | |||
9-135500987-C-G | Uncertain significance (Jun 14, 2023) | |||
9-135500990-C-A | Likely benign (Dec 07, 2023) | |||
9-135501000-G-A | Uncertain significance (Nov 04, 2023) | |||
9-135501001-C-T | not specified | Uncertain significance (Sep 24, 2024) | ||
9-135501019-G-A | Uncertain significance (Jun 06, 2023) | |||
9-135501025-G-A | not specified | Uncertain significance (Mar 31, 2024) | ||
9-135501026-C-G | Likely benign (Jun 12, 2023) | |||
9-135501043-C-A | MRPS2-related disorder | Benign (Jan 29, 2024) | ||
9-135501047-C-T | Likely benign (Nov 10, 2023) | |||
9-135501050-G-A | Likely benign (Jul 14, 2023) | |||
9-135501058-G-T | not specified | Uncertain significance (Feb 13, 2023) | ||
9-135501066-C-G | not specified | Likely benign (Sep 12, 2023) | ||
9-135501094-T-A | MRPS2-related disorder • not specified | Conflicting classifications of pathogenicity (Jan 26, 2023) | ||
9-135501109-C-T | Benign (Jun 22, 2023) | |||
9-135501132-G-A | MRPS2-related disorder | Likely benign (Jan 13, 2020) | ||
9-135501840-G-A | MRPS2-related disorder | Likely benign (Jun 17, 2024) | ||
9-135501877-A-G | Uncertain significance (Aug 30, 2022) | |||
9-135501878-G-A | MRPS2-related disorder | Likely benign (Apr 03, 2019) | ||
9-135501879-C-T | not specified | Uncertain significance (May 01, 2024) | ||
9-135501895-A-G | not specified | Uncertain significance (Sep 24, 2024) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
MRPS2 | protein_coding | protein_coding | ENST00000371785 | 4 | 4690 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
3.13e-7 | 0.101 | 125717 | 0 | 23 | 125740 | 0.0000915 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.0738 | 197 | 200 | 0.985 | 0.0000129 | 1925 |
Missense in Polyphen | 61 | 73.6 | 0.82881 | 650 | ||
Synonymous | -0.805 | 99 | 89.3 | 1.11 | 0.00000610 | 618 |
Loss of Function | -0.579 | 9 | 7.31 | 1.23 | 3.95e-7 | 82 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0000584 | 0.0000584 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000385 | 0.000381 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000989 | 0.0000967 |
Middle Eastern | 0.000385 | 0.000381 |
South Asian | 0.0000994 | 0.0000980 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Required for mitoribosome formation and stability, and mitochondrial translation. {ECO:0000269|PubMed:29576219}.;
- Disease
- DISEASE: Combined oxidative phosphorylation deficiency 36 (COXPD36) [MIM:617950]: An autosomal recessive, multisystem disease resulting from deficiencies of mitochondrial respiratory enzyme complexes and mitochondrial dysfunction. Clinical manifestations include sensorineural hearing impairment, mild developmental delay, hypoglycemia, and intellectual disability. {ECO:0000269|PubMed:29576219}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Ribosome - Homo sapiens (human);Mitochondrial translation initiation;Translation;Metabolism of proteins;Mitochondrial translation elongation;Mitochondrial translation termination;Mitochondrial translation
(Consensus)
Recessive Scores
- pRec
- 0.158
Intolerance Scores
- loftool
- 0.588
- rvis_EVS
- 0.6
- rvis_percentile_EVS
- 82.74
Haploinsufficiency Scores
- pHI
- 0.163
- hipred
- N
- hipred_score
- 0.472
- ghis
- 0.481
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.849
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Mrps2
- Phenotype
Gene ontology
- Biological process
- mitochondrial translation;mitochondrial ribosome assembly;mitochondrial translational elongation;mitochondrial translational termination
- Cellular component
- mitochondrion;mitochondrial inner membrane;mitochondrial small ribosomal subunit
- Molecular function
- structural constituent of ribosome