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RPL39

ribosomal protein L39, the group of L ribosomal proteins|Small nucleolar RNA protein coding host genes

Basic information

Region (hg38): X:119786503-119791630

Previous symbols: [ "RPL39P42" ]

Links

ENSG00000198918NCBI:6170OMIM:300899HGNC:10350Uniprot:P62891AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RPL39 gene.

  • Inborn genetic diseases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPL39 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
0
missense
1
clinvar
1
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 1 0 0

Variants in RPL39

This is a list of pathogenic ClinVar variants found in the RPL39 region.

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

Position Type Phenotype Significance ClinVar
X-119789983-C-T not specified Uncertain significance (Aug 16, 2022)2342793

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RPL39protein_codingprotein_codingENST00000361575 35140
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.5760.38300000.00
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.33217.80.1120.00000129329
Missense in Polyphen03.0716069
Synonymous0.18455.550.9013.54e-787
Loss of Function1.5102.640.002.04e-738

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)0.000.00
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

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
0.130

Intolerance Scores

loftool
rvis_EVS
0.15
rvis_percentile_EVS
63.81

Haploinsufficiency Scores

pHI
0.588
hipred
Y
hipred_score
0.601
ghis
0.541

Essentials

essential_gene_CRISPR
essential_gene_CRISPR2
essential_gene_gene_trap
E
gene_indispensability_pred
N
gene_indispensability_score
0.222

Mouse Genome Informatics

Gene name
Rpl39
Phenotype

Gene ontology

Biological process
nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;cytoplasmic translation;innate immune response in mucosa;translation;translational initiation;SRP-dependent cotranslational protein targeting to membrane;antibacterial humoral response;defense response to Gram-positive bacterium;antimicrobial humoral immune response mediated by antimicrobial peptide
Cellular component
extracellular space;cytosol;cytosolic large ribosomal subunit;polysomal ribosome
Molecular function
RNA binding;structural constituent of ribosome