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RPL4

ribosomal protein L4, the group of L ribosomal proteins|Small nucleolar RNA protein coding host genes

Basic information

Region (hg38): 15:66498014-66524532

Links

ENSG00000174444NCBI:6124OMIM:180479HGNC:10353Uniprot:P36578AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RPL4 gene.

  • Inborn genetic diseases (21 variants)
  • not provided (1 variants)
  • Exstrophy-epispadias complex (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPL4 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
missense
22
clinvar
22
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 22 1 0

Variants in RPL4

This is a list of pathogenic ClinVar variants found in the RPL4 region.

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

Position Type Phenotype Significance ClinVar
15-66499417-G-A not specified Uncertain significance (Feb 23, 2023)2488648
15-66499436-T-C not specified Uncertain significance (May 26, 2023)2508966
15-66499468-G-A not specified Uncertain significance (Nov 09, 2023)3156098
15-66499556-C-T not specified Uncertain significance (Jul 26, 2022)2303288
15-66499574-C-T not specified Uncertain significance (Dec 06, 2022)2333283
15-66499585-G-A not specified Uncertain significance (Feb 07, 2023)2464619
15-66499615-G-A not specified Uncertain significance (Jul 19, 2023)2598380
15-66499621-G-C not specified Uncertain significance (Feb 15, 2023)2454654
15-66499647-C-A not specified Uncertain significance (Oct 27, 2021)2257610
15-66500097-T-G not specified Uncertain significance (Mar 14, 2023)2496048
15-66500156-A-G not specified Uncertain significance (Nov 10, 2022)2373460
15-66500163-G-A not specified Uncertain significance (Jun 21, 2023)2604626
15-66500170-C-A not specified Uncertain significance (Aug 11, 2022)2387779
15-66500294-G-A not specified Uncertain significance (Feb 17, 2024)3156101
15-66500300-C-T not specified Uncertain significance (Mar 29, 2022)2280005
15-66501026-C-A not specified Uncertain significance (Oct 26, 2022)2319541
15-66501073-T-C not specified Uncertain significance (Dec 20, 2023)3156100
15-66501414-C-T not specified Uncertain significance (Jan 07, 2022)2271089
15-66501440-C-A Exstrophy-epispadias complex Uncertain significance (-)2628001
15-66501450-G-A not specified Uncertain significance (Dec 19, 2022)2216992
15-66501497-G-A not specified Uncertain significance (Jul 14, 2022)2298578
15-66501500-T-C not specified Uncertain significance (Oct 05, 2023)3156099
15-66501792-T-G not specified Uncertain significance (May 11, 2022)2204811
15-66501846-T-C not specified Uncertain significance (Apr 08, 2023)2517295
15-66501906-C-T High myopia Uncertain significance (Dec 17, 2018)623403

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RPL4protein_codingprotein_codingENST00000307961 1026516
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.000.000161125049021250510.00000800
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.272072650.7800.00001612762
Missense in Polyphen2674.9390.34695931
Synonymous-1.8310482.81.260.00000414862
Loss of Function4.62024.90.000.00000163258

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)0.000008850.00000884
Middle Eastern0.000.00
South Asian0.00003270.0000327
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;TNFalpha;Peptide chain elongation;Eukaryotic Translation Elongation;GTP hydrolysis and joining of the 60S ribosomal subunit;Cap-dependent Translation Initiation (Consensus)

Recessive Scores

pRec
0.379

Intolerance Scores

loftool
rvis_EVS
0.02
rvis_percentile_EVS
55.45

Haploinsufficiency Scores

pHI
0.992
hipred
Y
hipred_score
0.783
ghis
0.574

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
E
essential_gene_gene_trap
E
gene_indispensability_pred
E
gene_indispensability_score
0.935

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Rpl4
Phenotype

Gene ontology

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