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GeneBe

RPL5

ribosomal protein L5, the group of L ribosomal proteins|Protein phosphatase 1 regulatory subunits|Small nucleolar RNA protein coding host genes

Basic information

Region (hg38): 1:92832012-92841924

Links

ENSG00000122406NCBI:6125OMIM:603634HGNC:10360Uniprot:P46777AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • Diamond-Blackfan anemia 6 (Strong), mode of inheritance: AD
  • Diamond-Blackfan anemia (Supportive), mode of inheritance: AD
  • Diamond-Blackfan anemia 6 (Definitive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Diamond-Blackfan anemia 6ADCardiovascular; 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; 5764780; 19061985; 20301769; 23718193; 23812780

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RPL5 gene.

  • Diamond-Blackfan anemia (183 variants)
  • Diamond-Blackfan anemia 6 (79 variants)
  • not provided (31 variants)
  • not specified (19 variants)
  • - (4 variants)
  • RPL5-related condition (3 variants)
  • Diamond-Blackfan anemia 1 (3 variants)
  • Inborn genetic diseases (2 variants)
  • 17 conditions (1 variants)
  • See cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPL5 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
2
clinvar
30
missense
1
clinvar
69
clinvar
2
clinvar
72
nonsense
16
clinvar
2
clinvar
18
start loss
3
clinvar
3
frameshift
27
clinvar
7
clinvar
1
clinvar
35
inframe indel
1
clinvar
1
splice donor/acceptor (+/-2bp)
3
clinvar
6
clinvar
1
clinvar
10
splice region
2
8
9
19
non coding
1
clinvar
7
clinvar
28
clinvar
13
clinvar
49
Total 49 17 80 57 15

Variants in RPL5

This is a list of pathogenic ClinVar variants found in the RPL5 region.

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

Position Type Phenotype Significance ClinVar
1-92832041-C-A Diamond-Blackfan anemia 6 Uncertain significance (Jan 13, 2018)873660
1-92832045-T-A Diamond-Blackfan anemia 6 Uncertain significance (Jan 12, 2018)298196
1-92832051-C-G Diamond-Blackfan anemia 6 Uncertain significance (Jan 13, 2018)873661
1-92832053-C-G Diamond-Blackfan anemia 6 Likely benign (Jan 12, 2018)298197
1-92832057-G-T Diamond-Blackfan anemia 6 Benign (Sep 01, 2022)298198
1-92832060-C-G Diamond-Blackfan anemia 6 Benign (Jan 13, 2018)298199
1-92832063-C-G Diamond-Blackfan anemia 6 Benign (Jan 13, 2018)298200
1-92832067-G-A Diamond-Blackfan anemia 6 Benign (Jan 12, 2018)298201
1-92832069-C-A not provided (-)625274
1-92832069-C-G Diamond-Blackfan anemia 6 Uncertain significance (Jan 12, 2018)298202
1-92832073-A-C Diamond-Blackfan anemia 6 Benign (Jan 12, 2018)298203
1-92832077-C-T Diamond-Blackfan anemia 6 Likely benign (Jan 13, 2018)298204
1-92832097-C-A Diamond-Blackfan anemia 6 Benign (Jan 13, 2018)298205
1-92832109-C-T Diamond-Blackfan anemia 6 • not specified Likely benign (May 09, 2022)298206
1-92832113-G-A Diamond-Blackfan anemia 6 Uncertain significance (Jan 13, 2018)298207
1-92832115-A-C Diamond-Blackfan anemia Pathogenic (Jan 06, 2020)1069070
1-92832115-A-G Pathogenic (Feb 04, 2022)1700812
1-92832116-T-G Diamond-Blackfan anemia Pathogenic (Aug 22, 2022)2202776
1-92832117-G-A Diamond-Blackfan anemia Pathogenic (Jul 09, 2015)1736900
1-92832118-G-A Diamond-Blackfan anemia 6 Pathogenic/Likely pathogenic (May 04, 2023)1803120
1-92832120-G-A Diamond-Blackfan anemia Uncertain significance (Jul 28, 2023)1911206
1-92832120-G-C not specified • Diamond-Blackfan anemia • Diamond-Blackfan anemia 6 • Diamond-Blackfan anemia 1 • RPL5-related condition Benign/Likely benign (Jan 29, 2024)281749
1-92832120-G-T Diamond-Blackfan anemia Uncertain significance (Nov 10, 2020)1420907
1-92832122-G-A Diamond-Blackfan anemia Uncertain significance (May 29, 2022)2098046
1-92832122-G-C Diamond-Blackfan anemia Uncertain significance (Jun 11, 2023)2711753

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RPL5protein_codingprotein_codingENST00000370321 89900
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9980.0022400000.00
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.901011710.5910.000009421962
Missense in Polyphen2955.4280.5232679
Synonymous-0.2885855.31.050.00000280539
Loss of Function3.92017.90.000.00000111208

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:12962325, PubMed:19061985, PubMed:24120868, PubMed:23636399). 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). {ECO:0000269|PubMed:12962325, ECO:0000269|PubMed:19061985, ECO:0000269|PubMed:23636399, ECO:0000269|PubMed:24120868}.;
Disease
DISEASE: Diamond-Blackfan anemia 6 (DBA6) [MIM:612561]: 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);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;p53 pathway (Consensus)

Recessive Scores

pRec
0.206

Intolerance Scores

loftool
rvis_EVS
-0.03
rvis_percentile_EVS
51.4

Haploinsufficiency Scores

pHI
0.263
hipred
Y
hipred_score
0.783
ghis
0.595

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
N
essential_gene_gene_trap
E
gene_indispensability_pred
E
gene_indispensability_score
0.961

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Rpl5
Phenotype

Zebrafish Information Network

Gene name
rpl5a
Affected structure
nucleate erythrocyte
Phenotype tag
abnormal
Phenotype quality
decreased amount

Gene ontology

Biological process
ribosomal large subunit assembly;nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;rRNA processing;translation;translational initiation;SRP-dependent cotranslational protein targeting to membrane;positive regulation of gene expression;ribosomal large subunit biogenesis;positive regulation of translation;protein stabilization;regulation of signal transduction 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
nucleus;nucleoplasm;nucleolus;cytoplasm;endoplasmic reticulum;cytosol;focal adhesion;membrane;cytosolic large ribosomal subunit;protein-containing complex;extracellular exosome;ribonucleoprotein complex
Molecular function
RNA binding;mRNA 3'-UTR binding;structural constituent of ribosome;protein binding;5S rRNA binding;ubiquitin protein ligase binding;mRNA 5'-UTR binding;ubiquitin ligase inhibitor activity