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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

ENSG00000114686NCBI:11222OMIM:607118HGNC:10379Uniprot:P09001AlphaFoldGenCCjaxSfariGnomADPubmed

Phenotypes

GenCC

Source: genCC

  • combined oxidative phosphorylation defect type 9 (Limited), mode of inheritance: AR
  • mitochondrial disease (Moderate), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Combined oxidative phosphorylation deficiency 9ARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingBiochemical; Cardiovascular; Gastrointestinal; Musculoskeletal; Neurologic21786366

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MRPL3 gene.

  • 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)link
3-131462737-T-C Uncertain significance (May 27, 2022)link
3-131462751-G-A Inborn genetic diseases Uncertain significance (Dec 02, 2022)link
3-131462785-G-A Inborn genetic diseases Uncertain significance (Feb 28, 2023)link
3-131462789-T-C Likely benign (Apr 19, 2018)link
3-131462816-T-C Likely benign (Dec 31, 2019)link
3-131462820-G-C Combined oxidative phosphorylation defect type 9 Likely pathogenic (Dec 27, 2019)link
3-131462825-T-C not specified Benign (Aug 09, 2022)link
3-131462832-T-G Uncertain significance (May 31, 2022)link
3-131462839-C-T Benign/Likely benign (May 01, 2023)link
3-131462868-T-C Inborn genetic diseases Uncertain significance (Jun 09, 2022)link
3-131468049-CA-C Benign (Aug 06, 2019)link
3-131468063-GA-G Benign (Aug 06, 2019)link
3-131468084-T-C not specified Likely benign (Jul 29, 2022)link
3-131468099-A-G not specified Benign (Oct 27, 2022)link
3-131468100-G-A Likely benign (Dec 31, 2019)link
3-131468101-C-G Combined oxidative phosphorylation defect type 9 not provided (-)link
3-131468123-A-G Combined oxidative phosphorylation defect type 9 Uncertain significance (Oct 04, 2022)link
3-131468161-C-T Uncertain significance (Oct 31, 2022)link
3-131469414-T-C Likely benign (Nov 27, 2018)link
3-131469474-A-G Likely benign (Jul 15, 2018)link
3-131469533-TAC-T Benign (Aug 06, 2019)link
3-131469533-T-TAC Likely benign (Aug 15, 2019)link
3-131469684-T-G not specified Benign (Oct 30, 2022)link
3-131469687-AAC-A Likely benign (Sep 20, 2022)link

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
MRPL3protein_codingprotein_codingENST00000264995 1040772
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.30e-120.04941256930551257480.000219
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.1602001941.030.000009732248
Missense in Polyphen7278.8990.91256947
Synonymous-0.9638271.61.140.00000385671
Loss of Function0.2481920.20.9409.56e-7239

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0004720.000470
Ashkenazi Jewish0.0002980.000298
East Asian0.00005480.0000544
Finnish0.00009290.0000924
European (Non-Finnish)0.0002480.000246
Middle Eastern0.00005480.0000544
South Asian0.0001680.000163
Other0.0002130.000163

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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