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RPL3

ribosomal protein L3, the group of L ribosomal proteins|Small nucleolar RNA protein coding host genes

Basic information

Region (hg38): 22:39312881-39320389

Links

ENSG00000100316NCBI:6122OMIM:604163HGNC:10332Uniprot:P39023AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RPL3 gene.

  • Inborn genetic diseases (11 variants)
  • not provided (5 variants)
  • not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPL3 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
1
clinvar
2
missense
11
clinvar
1
clinvar
12
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
1
1
2
non coding
1
clinvar
1
Total 0 0 11 2 2

Variants in RPL3

This is a list of pathogenic ClinVar variants found in the RPL3 region.

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

Position Type Phenotype Significance ClinVar
22-39312960-C-T Inborn genetic diseases Likely benign (Feb 10, 2023)2482982
22-39313286-G-A Inborn genetic diseases Uncertain significance (Oct 12, 2022)2220086
22-39313303-A-G Inborn genetic diseases Uncertain significance (Aug 12, 2021)2243519
22-39313642-G-A Inborn genetic diseases Uncertain significance (Jun 27, 2022)2354315
22-39314213-ATGAACAAGAAGGG-A Uncertain significance (Nov 01, 2023)2672909
22-39314788-G-A Likely benign (Oct 01, 2022)2653146
22-39315393-C-T Inborn genetic diseases Uncertain significance (Jun 30, 2022)2299564
22-39315424-A-C Inborn genetic diseases Uncertain significance (Nov 22, 2021)2383893
22-39316720-T-C Inborn genetic diseases Uncertain significance (Dec 16, 2022)2336187
22-39316756-T-C Inborn genetic diseases Uncertain significance (Sep 16, 2021)2249856
22-39316911-G-A Benign (Dec 01, 2022)2653147
22-39317464-T-C Inborn genetic diseases Uncertain significance (Feb 28, 2023)2460581
22-39317473-A-T not specified Uncertain significance (May 04, 2022)1685078
22-39317633-C-CA Benign (Mar 29, 2018)781529
22-39318469-G-A Inborn genetic diseases Uncertain significance (Apr 06, 2023)2513989
22-39318485-C-T Benign (Nov 05, 2019)1258969
22-39318527-G-C Inborn genetic diseases Uncertain significance (Apr 13, 2022)2283787

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RPL3protein_codingprotein_codingENST00000216146 107508
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9940.00559125741011257420.00000398
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.561782470.7210.00001462650
Missense in Polyphen2546.9480.53251601
Synonymous-2.4511787.81.330.00000473769
Loss of Function3.92119.80.05059.71e-7238

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000008790.00000879
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: The L3 protein is a component of the large subunit of cytoplasmic ribosomes. {ECO:0000305|PubMed:12962325}.;
Pathway
Ribosome - Homo sapiens (human);Cytoplasmic Ribosomal Proteins;SRP-dependent cotranslational protein targeting to membrane;Eukaryotic Translation Initiation;Eukaryotic Translation Termination;Translation;Selenocysteine synthesis;Metabolism of proteins;Metabolism of amino acids and derivatives;Metabolism of RNA;Formation of a pool of free 40S subunits;Metabolism;Nonsense-Mediated Decay (NMD);Selenoamino acid metabolism;Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC);Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC);L13a-mediated translational silencing of Ceruloplasmin expression;Peptide chain elongation;Eukaryotic Translation Elongation;GTP hydrolysis and joining of the 60S ribosomal subunit;Cap-dependent Translation Initiation (Consensus)

Recessive Scores

pRec
0.273

Intolerance Scores

loftool
rvis_EVS
-0.76
rvis_percentile_EVS
13.33

Haploinsufficiency Scores

pHI
0.304
hipred
Y
hipred_score
0.783
ghis
0.636

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
E
essential_gene_gene_trap
E
gene_indispensability_pred
E
gene_indispensability_score
0.946

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Rpl3
Phenotype

Zebrafish Information Network

Gene name
rpl3
Affected structure
exocrine pancreas
Phenotype tag
abnormal
Phenotype quality
decreased size

Gene ontology

Biological process
ribosomal large subunit assembly;nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;translation;translational initiation;SRP-dependent cotranslational protein targeting to membrane;cellular response to interleukin-4
Cellular component
nucleus;nucleolus;cytoplasm;cytosol;focal adhesion;cytosolic large ribosomal subunit;protein-containing complex;extracellular exosome
Molecular function
RNA binding;structural constituent of ribosome;protein binding