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

ENSG00000100316 ∙ NCBI:6122 ∙ OMIM:604163 ∙ HGNC:10332 ∙ Uniprot:P39023 ∙ 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 RPL3 gene.

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	1	2
missense			17	1		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1		1	2
non coding			1		1	2
Total	0	0	18	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		not specified	Likely benign (Feb 10, 2023)
22-39313212-C-T		not specified	Uncertain significance (Jul 06, 2021)
22-39313286-G-A		not specified	Uncertain significance (Oct 12, 2022)
22-39313289-G-A		not specified	Uncertain significance (Oct 20, 2023)
22-39313303-A-G		not specified	Uncertain significance (Aug 12, 2021)
22-39313642-G-A		not specified	Uncertain significance (Jun 27, 2022)
22-39314213-ATGAACAAGAAGGG-A			Uncertain significance (Nov 01, 2023)
22-39314788-G-A			Likely benign (Oct 01, 2022)
22-39315393-C-T		not specified	Uncertain significance (Jun 30, 2022)
22-39315424-A-C		not specified	Uncertain significance (Nov 22, 2021)
22-39315444-C-T		not specified	Uncertain significance (Nov 09, 2023)
22-39316720-T-C		not specified	Uncertain significance (Dec 16, 2022)
22-39316756-T-C		not specified	Uncertain significance (Sep 16, 2021)
22-39316765-T-C		not specified	Uncertain significance (Jan 03, 2024)
22-39316911-G-A			Benign (Dec 01, 2022)
22-39317464-T-C		not specified	Uncertain significance (Feb 28, 2023)
22-39317468-T-C		not specified	Uncertain significance (Jan 24, 2024)
22-39317473-A-T		not specified	Uncertain significance (May 04, 2022)
22-39317633-C-CA			Benign (Mar 29, 2018)
22-39318435-G-C		not specified	Uncertain significance (Sep 29, 2023)
22-39318469-G-A		not specified	Uncertain significance (Apr 06, 2023)
22-39318485-C-T			Benign (Nov 05, 2019)
22-39318486-G-A		not specified	Uncertain significance (May 25, 2022)
22-39318527-G-C		not specified	Uncertain significance (Apr 13, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RPL3	protein_coding	protein_coding	ENST00000216146	10	7508

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.994	0.00559	125741	0	1	125742	0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.56	178	247	0.721	0.0000146	2650
Missense in Polyphen		25	46.948	0.53251		601
Synonymous	-2.45	117	87.8	1.33	0.00000473	769
Loss of Function	3.92	1	19.8	0.0505	9.71e-7	238

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)	0.00000879	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

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

• 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

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

Mouse Genome Informatics

• Gene name: Rpl3

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