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GeneBe

RPL11

ribosomal protein L11, the group of L ribosomal proteins

Basic information

Region (hg38): 1:23691741-23696835

Links

ENSG00000142676NCBI:6135OMIM:604175HGNC:10301Uniprot:P62913AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Diamond-Blackfan anemia 7ADCardiovascular; Hematologic; OncologicSpecific 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 managementCardiovascular; Craniofacial; Hematologic; Musculoskeletal; Oncologic; Renal16317735; 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
clinvar
27
clinvar
3
clinvar
31
missense
23
clinvar
23
nonsense
4
clinvar
4
start loss
0
frameshift
16
clinvar
2
clinvar
1
clinvar
19
inframe indel
3
clinvar
3
splice donor/acceptor (+/-2bp)
5
clinvar
5
clinvar
1
clinvar
11
splice region
5
6
11
non coding
3
clinvar
18
clinvar
15
clinvar
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)138926
1-23691810-T-C Diamond-Blackfan anemia 7 Uncertain significance (Jan 12, 2018)296814
1-23691817-C-T RPL11-related condition Likely benign (May 30, 2023)3040903
1-23691827-G-T Diamond-Blackfan anemia Uncertain significance (Oct 11, 2017)532178
1-23691828-C-T Diamond-Blackfan anemia Uncertain significance (Jul 19, 2022)579074
1-23691831-T-C Diamond-Blackfan anemia Pathogenic (Dec 26, 2014)1751021
1-23691832-G-A Diamond-Blackfan anemia Uncertain significance (Nov 19, 2023)2739493
1-23691837-G-C not specified • Diamond-Blackfan anemia Likely benign (Aug 22, 2022)698043
1-23691837-G-T Diamond-Blackfan anemia Likely benign (Dec 18, 2023)2893716
1-23691838-C-T Diamond-Blackfan anemia Benign (Oct 02, 2022)1632651
1-23691839-T-A Diamond-Blackfan anemia Likely benign (Jan 05, 2024)2994422
1-23691841-G-C Diamond-Blackfan anemia Likely benign (Nov 07, 2022)2713583
1-23691843-A-G Diamond-Blackfan anemia Likely benign (Jan 25, 2024)1567257
1-23691844-C-T Diamond-Blackfan anemia Likely benign (Dec 04, 2023)1628457
1-23691845-C-G Diamond-Blackfan anemia Likely benign (Nov 28, 2022)2105799
1-23691845-C-T Diamond-Blackfan anemia Likely benign (Jan 26, 2024)1567321
1-23691847-G-A Diamond-Blackfan anemia Benign (Jan 03, 2023)2203031
1-23691847-GG-AT Diamond-Blackfan anemia Likely benign (Oct 04, 2023)1627562
1-23691848-G-C Diamond-Blackfan anemia Likely benign (Jul 07, 2023)2875516
1-23691848-G-T not specified • Diamond-Blackfan anemia Benign/Likely benign (Oct 18, 2023)508925
1-23691849-A-T Diamond-Blackfan anemia Likely benign (May 22, 2022)1902486
1-23691879-G-T not specified Benign (Jan 20, 2016)379217
1-23691897-G-T Benign (Mar 03, 2015)1243261
1-23692463-T-C Benign (Mar 03, 2015)1251916
1-23692475-T-G Benign (Mar 03, 2015)1289189

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RPL11protein_codingprotein_codingENST00000374550 64647
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9610.039000000.00
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.695198.10.5200.000005401161
Missense in Polyphen623.4790.25555328
Synonymous-1.404433.71.310.00000166327
Loss of Function2.95010.10.005.03e-7123

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

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

loftool
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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Rpl11
Phenotype

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