RPL11

ribosomal protein L11, the group of L ribosomal proteins

Basic information

Region (hg38): 1:23691741-23696835

Links

ENSG00000142676 ∙ NCBI:6135 ∙ OMIM:604175 ∙ HGNC:10301 ∙ Uniprot:P62913 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Diamond-Blackfan anemia 7 (Strong), mode of inheritance: AD
• Diamond-Blackfan anemia (Supportive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Diamond-Blackfan anemia 7	AD	Cardiovascular; Hematologic; Oncologic	Specific treatment of anemia (eg, steroids, regular transfusions) can be effective; Surveillance for and early treatment of malignancy may allow early detection and management; Individuals with DBA may manifest a variety of congenital malformations (eg, cardiac anomalies), and awareness may allow prompt detection and management	Cardiovascular; Craniofacial; Hematologic; Musculoskeletal; Oncologic; Renal	16317735; 19061985; 20301769; 23718193; 23812780

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RPL11 gene.

• Diamond-Blackfan anemia (118 variants)
• Diamond-Blackfan anemia 7 (32 variants)
• not provided (19 variants)
• not specified (6 variants)
• RPL11-related condition (1 variants)
• Inborn genetic diseases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPL11 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	27	3	31
missense			23			23
nonsense	4					4
start loss						0
frameshift	16	2	1			19
inframe indel			3			3
splice donor/acceptor (+/-2bp)	5	5	1			11
splice region			5	6		11
non coding			3	18	15	36
Total	25	7	32	45	18

Variants in RPL11

This is a list of pathogenic ClinVar variants found in the RPL11 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-23691787-C-G		Diamond-Blackfan anemia • Diamond-Blackfan anemia 7	Benign (Nov 07, 2021)
1-23691810-T-C		Diamond-Blackfan anemia 7	Uncertain significance (Jan 12, 2018)
1-23691817-C-T		RPL11-related disorder	Likely benign (May 30, 2023)
1-23691827-G-T		Diamond-Blackfan anemia	Uncertain significance (Oct 11, 2017)
1-23691828-C-T		Diamond-Blackfan anemia	Uncertain significance (Jul 19, 2022)
1-23691831-T-C		Diamond-Blackfan anemia	Pathogenic (Dec 26, 2014)
1-23691832-G-A		Diamond-Blackfan anemia	Uncertain significance (Nov 19, 2023)
1-23691837-G-C		not specified • Diamond-Blackfan anemia	Likely benign (Aug 22, 2022)
1-23691837-G-T		Diamond-Blackfan anemia	Likely benign (Dec 18, 2023)
1-23691838-C-T		Diamond-Blackfan anemia	Benign (Oct 02, 2022)
1-23691839-T-A		Diamond-Blackfan anemia	Likely benign (Jan 05, 2024)
1-23691841-G-C		Diamond-Blackfan anemia	Likely benign (Nov 07, 2022)
1-23691843-A-G		Diamond-Blackfan anemia	Likely benign (Jan 25, 2024)
1-23691844-C-T		Diamond-Blackfan anemia	Likely benign (Dec 04, 2023)
1-23691845-C-G		Diamond-Blackfan anemia	Likely benign (Nov 28, 2022)
1-23691845-C-T		Diamond-Blackfan anemia	Likely benign (Jan 26, 2024)
1-23691847-G-A		Diamond-Blackfan anemia	Benign (Jan 03, 2023)
1-23691847-GG-AT		Diamond-Blackfan anemia	Likely benign (Oct 04, 2023)
1-23691848-G-C		Diamond-Blackfan anemia	Likely benign (Jul 07, 2023)
1-23691848-G-T		not specified • Diamond-Blackfan anemia	Benign/Likely benign (Oct 18, 2023)
1-23691849-A-T		Diamond-Blackfan anemia	Likely benign (May 22, 2022)
1-23691879-G-T		not specified	Benign (Jan 20, 2016)
1-23691897-G-T			Benign (Mar 03, 2015)
1-23692463-T-C			Benign (Mar 03, 2015)
1-23692475-T-G			Benign (Mar 03, 2015)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RPL11	protein_coding	protein_coding	ENST00000374550	6	4647

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.961	0.0390	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.69	51	98.1	0.520	0.00000540	1161
Missense in Polyphen		6	23.479	0.25555		328
Synonymous	-1.40	44	33.7	1.31	0.00000166	327
Loss of Function	2.95	0	10.1	0.00	5.03e-7	123

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the ribosome, a large ribonucleoprotein complex responsible for the synthesis of proteins in the cell. The small ribosomal subunit (SSU) binds messenger RNAs (mRNAs) and translates the encoded message by selecting cognate aminoacyl- transfer RNA (tRNA) molecules. The large subunit (LSU) contains the ribosomal catalytic site termed the peptidyl transferase center (PTC), which catalyzes the formation of peptide bonds, thereby polymerizing the amino acids delivered by tRNAs into a polypeptide chain. The nascent polypeptides leave the ribosome through a tunnel in the LSU and interact with protein factors that function in enzymatic processing, targeting, and the membrane insertion of nascent chains at the exit of the ribosomal tunnel. As part of the 5S RNP/5S ribonucleoprotein particle it is an essential component of the LSU, required for its formation and the maturation of rRNAs (PubMed:19061985, PubMed:12962325, PubMed:24120868). It also couples ribosome biogenesis to p53/TP53 activation. As part of the 5S RNP it accumulates in the nucleoplasm and inhibits MDM2, when ribosome biogenesis is perturbed, mediating the stabilization and the activation of TP53 (PubMed:24120868). Promotes nucleolar location of PML (By similarity). {ECO:0000250|UniProtKB:Q9CXW4, ECO:0000269|PubMed:12962325, ECO:0000269|PubMed:19061985, ECO:0000269|PubMed:24120868}.
• Disease: DISEASE: Diamond-Blackfan anemia 7 (DBA7) [MIM:612562]: A form of Diamond-Blackfan anemia, a congenital non-regenerative hypoplastic anemia that usually presents early in infancy. Diamond-Blackfan anemia is characterized by a moderate to severe macrocytic anemia, erythroblastopenia, and an increased risk of malignancy. 30 to 40% of Diamond-Blackfan anemia patients present with short stature and congenital anomalies, the most frequent being craniofacial (Pierre-Robin syndrome and cleft palate), thumb and urogenital anomalies. {ECO:0000269|PubMed:19061985, ECO:0000269|PubMed:19191325}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Ribosome - Homo sapiens (human);MET in type 1 papillary renal cell carcinoma;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;Validated targets of C-MYC transcriptional activation;p53 pathway (Consensus)

Intolerance Scores

• rvis_EVS: -0.05
• rvis_percentile_EVS: 49.39

Haploinsufficiency Scores

• pHI: 0.913
• hipred: Y
• hipred_score: 0.756
• ghis: 0.601

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.912

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rpl11

Zebrafish Information Network

• Gene name: rpl11
• Affected structure: erythroid lineage cell
• Phenotype tag: ameliorated
• Phenotype quality: decreased amount

Gene ontology

• Biological process: ribosomal large subunit assembly;nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;cytoplasmic translation;rRNA processing;translation;translational initiation;protein targeting;SRP-dependent cotranslational protein targeting to membrane;positive regulation of gene expression;positive regulation of protein binding;negative regulation of proteasomal ubiquitin-dependent protein catabolic process;protein localization to nucleus;ribosomal large subunit biogenesis;protein stabilization;regulation of signal transduction by p53 class mediator;positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator;negative regulation of ubiquitin protein ligase activity;negative regulation of ubiquitin-dependent protein catabolic process;negative regulation of protein neddylation
• Cellular component: nucleoplasm;nucleolus;cytoplasm;cytosol;membrane;cytosolic large ribosomal subunit;protein-containing complex;polysomal ribosome;extracellular exosome
• Molecular function: RNA binding;structural constituent of ribosome;protein binding;5S rRNA binding;ubiquitin protein ligase binding;ubiquitin ligase inhibitor activity