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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:P09001AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • combined oxidative phosphorylation defect type 9 (Limited), mode of inheritance: AR
  • mitochondrial disease (Moderate), mode of inheritance: AR
  • combined oxidative phosphorylation defect type 9 (Strong), 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 (78 variants)
  • Inborn genetic diseases (12 variants)
  • not specified (11 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.

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
1
clinvar
8
clinvar
3
clinvar
12
missense
1
clinvar
30
clinvar
4
clinvar
1
clinvar
36
nonsense
2
clinvar
2
start loss
0
frameshift
1
clinvar
1
inframe indel
0
splice donor/acceptor (+/-2bp)
1
clinvar
1
splice region
3
1
4
non coding
1
clinvar
18
clinvar
17
clinvar
36
Total 1 2 34 30 21

Highest pathogenic variant AF is 0.0000132

Variants in MRPL3

This is a list of pathogenic ClinVar variants found in the MRPL3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
3-131462637-G-A Likely benign (Jan 28, 2019)1193072
3-131462737-T-C Uncertain significance (Nov 09, 2023)425313
3-131462751-G-A Inborn genetic diseases Uncertain significance (Dec 02, 2022)2331996
3-131462761-C-T Uncertain significance (Oct 14, 2022)2983989
3-131462785-G-A Inborn genetic diseases Conflicting classifications of pathogenicity (Nov 27, 2023)1203624
3-131462789-T-C Likely benign (Apr 19, 2018)681599
3-131462816-T-C Likely benign (Oct 11, 2023)704125
3-131462820-G-C Combined oxidative phosphorylation defect type 9 Likely pathogenic (Dec 27, 2019)30643
3-131462825-T-C not specified Benign (Jan 15, 2024)386054
3-131462832-T-G Uncertain significance (Nov 08, 2022)1905248
3-131462839-C-T Benign/Likely benign (Jan 24, 2024)374558
3-131462868-T-C Inborn genetic diseases Uncertain significance (Jun 09, 2022)2294630
3-131468049-CA-C Benign (Aug 06, 2019)1239761
3-131468063-GA-G Benign (Aug 06, 2019)1292149
3-131468084-T-C not specified Likely benign (Nov 07, 2023)507991
3-131468099-A-G not specified Benign (Jan 23, 2024)380562
3-131468100-G-A MRPL3-related condition Likely benign (Jan 15, 2024)507537
3-131468101-C-G Combined oxidative phosphorylation defect type 9 not provided (-)441035
3-131468123-A-G Combined oxidative phosphorylation defect type 9 Uncertain significance (Oct 04, 2022)1027733
3-131468161-C-T Uncertain significance (Oct 31, 2022)1987911
3-131469414-T-C Likely benign (Nov 27, 2018)1211509
3-131469474-A-G Likely benign (Jul 15, 2018)1217728
3-131469533-TAC-T Benign (Aug 06, 2019)1259936
3-131469533-T-TAC Likely benign (Aug 15, 2019)1198044
3-131469684-T-G not specified Benign (Jan 30, 2024)380042

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