MRPL3
mitochondrial ribosomal protein L3, the group of Small nucleolar RNA protein coding host genes|Large subunit mitochondrial ribosomal proteins|Mitochondrial ribosomal proteins
Basic information
Region (hg38): 3:131462211-131502983
Previous symbols: [ "RPML3" ]
Links
Phenotypes
GenCC
Source:
- combined oxidative phosphorylation defect type 9 (Limited), mode of inheritance: AR
- mitochondrial disease (Moderate), mode of inheritance: AR
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Combined oxidative phosphorylation deficiency 9 | 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 | Biochemical; Cardiovascular; Gastrointestinal; Musculoskeletal; Neurologic | 21786366 |
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (76 variants)
- not specified (11 variants)
- Inborn genetic diseases (6 variants)
- Combined oxidative phosphorylation defect type 9 (4 variants)
- Neonatal encephalopathy (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the MRPL3 gene is commonly pathogenic or not.
Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
---|---|---|---|---|---|---|
synonymous | 1 | 7 | 3 | 11 | ||
missense | 1 | 25 | 2 | 1 | 29 | |
nonsense | 2 | 2 | ||||
start loss | 0 | |||||
frameshift | 1 | 1 | 2 | |||
inframe indel | 1 | 1 | ||||
splice variant | 1 | 4 | 1 | 6 | ||
non coding | 1 | 16 | 17 | 34 | ||
Total | 2 | 2 | 29 | 30 | 22 |
Highest pathogenic variant AF is 0.0000132
Variants in MRPL3
This is a list of pathogenic ClinVar variants found in the MRPL3 region.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
3-131462637-G-A | Likely benign (Jan 28, 2019) | |||
3-131462737-T-C | Uncertain significance (May 27, 2022) | |||
3-131462751-G-A | Inborn genetic diseases | Uncertain significance (Dec 02, 2022) | ||
3-131462785-G-A | Inborn genetic diseases | Uncertain significance (Feb 28, 2023) | ||
3-131462789-T-C | Likely benign (Apr 19, 2018) | |||
3-131462816-T-C | Likely benign (Dec 31, 2019) | |||
3-131462820-G-C | Combined oxidative phosphorylation defect type 9 | Likely pathogenic (Dec 27, 2019) | ||
3-131462825-T-C | not specified | Benign (Aug 09, 2022) | ||
3-131462832-T-G | Uncertain significance (May 31, 2022) | |||
3-131462839-C-T | Benign/Likely benign (May 01, 2023) | |||
3-131462868-T-C | Inborn genetic diseases | Uncertain significance (Jun 09, 2022) | ||
3-131468049-CA-C | Benign (Aug 06, 2019) | |||
3-131468063-GA-G | Benign (Aug 06, 2019) | |||
3-131468084-T-C | not specified | Likely benign (Jul 29, 2022) | ||
3-131468099-A-G | not specified | Benign (Oct 27, 2022) | ||
3-131468100-G-A | Likely benign (Dec 31, 2019) | |||
3-131468101-C-G | Combined oxidative phosphorylation defect type 9 | not provided (-) | ||
3-131468123-A-G | Combined oxidative phosphorylation defect type 9 | Uncertain significance (Oct 04, 2022) | ||
3-131468161-C-T | Uncertain significance (Oct 31, 2022) | |||
3-131469414-T-C | Likely benign (Nov 27, 2018) | |||
3-131469474-A-G | Likely benign (Jul 15, 2018) | |||
3-131469533-TAC-T | Benign (Aug 06, 2019) | |||
3-131469533-T-TAC | Likely benign (Aug 15, 2019) | |||
3-131469684-T-G | not specified | Benign (Oct 30, 2022) | ||
3-131469687-AAC-A | Likely benign (Sep 20, 2022) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
MRPL3 | protein_coding | protein_coding | ENST00000264995 | 10 | 40772 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.30e-12 | 0.0494 | 125693 | 0 | 55 | 125748 | 0.000219 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -0.160 | 200 | 194 | 1.03 | 0.00000973 | 2248 |
Missense in Polyphen | 72 | 78.899 | 0.91256 | 947 | ||
Synonymous | -0.963 | 82 | 71.6 | 1.14 | 0.00000385 | 671 |
Loss of Function | 0.248 | 19 | 20.2 | 0.940 | 9.56e-7 | 239 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000472 | 0.000470 |
Ashkenazi Jewish | 0.000298 | 0.000298 |
East Asian | 0.0000548 | 0.0000544 |
Finnish | 0.0000929 | 0.0000924 |
European (Non-Finnish) | 0.000248 | 0.000246 |
Middle Eastern | 0.0000548 | 0.0000544 |
South Asian | 0.000168 | 0.000163 |
Other | 0.000213 | 0.000163 |
dbNSFP
Source:
- Disease
- DISEASE: Combined oxidative phosphorylation deficiency 9 (COXPD9) [MIM:614582]: A mitochondrial disease characterized by failure to thrive, poor feeding, hypertrophic cardiomyopathy, hepatomegaly, and psychomotor retardation. Death in infancy has been observed in some cases. {ECO:0000269|PubMed:21786366}. 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
- 0.131
Intolerance Scores
- loftool
- 0.889
- rvis_EVS
- -0.09
- rvis_percentile_EVS
- 46.92
Haploinsufficiency Scores
- pHI
- 0.160
- hipred
- N
- hipred_score
- 0.486
- ghis
- 0.638
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.815
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Mrpl3
- Phenotype
Gene ontology
- Biological process
- translation;mitochondrial translational elongation;mitochondrial translational termination
- Cellular component
- mitochondrion;mitochondrial inner membrane;mitochondrial large ribosomal subunit
- Molecular function
- RNA binding;structural constituent of ribosome