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

ENSG00000174444 ∙ NCBI:6124 ∙ OMIM:180479 ∙ HGNC:10353 ∙ Uniprot:P36578 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

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		1
missense			26			26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	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)
15-66499436-T-C		not specified	Uncertain significance (May 26, 2023)
15-66499468-G-A		not specified	Uncertain significance (Nov 09, 2023)
15-66499556-C-T		not specified	Uncertain significance (Jul 26, 2022)
15-66499574-C-T		not specified	Uncertain significance (Dec 06, 2022)
15-66499585-G-A		not specified	Uncertain significance (Feb 07, 2023)
15-66499615-G-A		not specified	Uncertain significance (Jul 19, 2023)
15-66499621-G-C		not specified	Uncertain significance (Feb 15, 2023)
15-66499647-C-A		not specified	Uncertain significance (Oct 27, 2021)
15-66500097-T-G		not specified	Uncertain significance (Mar 14, 2023)
15-66500156-A-G		not specified	Uncertain significance (Nov 10, 2022)
15-66500163-G-A		not specified	Uncertain significance (Jun 21, 2023)
15-66500170-C-A		not specified	Uncertain significance (Aug 11, 2022)
15-66500294-G-A		not specified	Uncertain significance (Feb 17, 2024)
15-66500300-C-T		not specified	Uncertain significance (Mar 29, 2022)
15-66501026-C-A		not specified	Uncertain significance (Oct 26, 2022)
15-66501073-T-C		not specified	Uncertain significance (Dec 20, 2023)
15-66501414-C-T		not specified	Uncertain significance (Jan 07, 2022)
15-66501440-C-A		Exstrophy-epispadias complex	Uncertain significance (-)
15-66501450-G-A		not specified	Uncertain significance (Dec 19, 2022)
15-66501497-G-A		not specified	Uncertain significance (Jul 14, 2022)
15-66501500-T-C		not specified	Uncertain significance (Oct 05, 2023)
15-66501792-T-G		not specified	Uncertain significance (May 11, 2022)
15-66501846-T-C		not specified	Uncertain significance (Apr 08, 2023)
15-66501906-C-T		High myopia	Uncertain significance (Dec 17, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RPL4	protein_coding	protein_coding	ENST00000307961	10	26516

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000161	125049	0	2	125051	0.00000800

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.27	207	265	0.780	0.0000161	2762
Missense in Polyphen		26	74.939	0.34695		931
Synonymous	-1.83	104	82.8	1.26	0.00000414	862
Loss of Function	4.62	0	24.9	0.00	0.00000163	258

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000885	0.00000884
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

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

• 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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Rpl4

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