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GeneBe

RPL15

ribosomal protein L15, the group of L ribosomal proteins

Basic information

Region (hg38): 3:23916590-23924374

Links

ENSG00000174748NCBI:6138OMIM:604174HGNC:10306Uniprot:P61313AlphaFoldGenCCjaxSfariGnomADPubmed

Phenotypes

GenCC

Source: genCC

  • Diamond-Blackfan anemia 12 (Strong), mode of inheritance: AD
  • Diamond-Blackfan anemia 12 (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 12ADCardiovascular; 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; Hematologic; Musculoskeletal; Neurologic; Oncologic20301769; 23812780

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RPL15 gene.

  • not provided (89 variants)
  • not specified (9 variants)
  • Diamond-Blackfan anemia 12 (6 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 RPL15 gene is commonly pathogenic or not.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous 2 22 5 29
missense 1 36 1 38
nonsense 1 1
start loss 0
frameshift 1 1
inframe indel 0
splice variant 1 1 6 2 10
non coding 2 7 8 17
Total 3 1 41 35 16

Variants in RPL15

This is a list of pathogenic ClinVar variants found in the RPL15 region.

Position Type Phenotype Significance ClinVar
3-23917732-A-C Likely benign (Dec 21, 2018)link
3-23917766-T-C Likely benign (Aug 09, 2018)link
3-23917859-G-C not specified Uncertain significance (Jan 03, 2019)link
3-23917877-C-T Likely benign (Dec 16, 2019)link
3-23917888-T-C Diamond-Blackfan anemia 12 Pathogenic (May 18, 2023)link
3-23917906-C-G Uncertain significance (Sep 19, 2022)link
3-23917914-A-G Uncertain significance (Jul 19, 2022)link
3-23917934-C-G not specified Benign (Nov 02, 2022)link
3-23917944-C-A Uncertain significance (Jun 30, 2022)link
3-23917944-C-T Diamond-Blackfan anemia 12 Pathogenic (May 18, 2023)link
3-23917946-G-T Uncertain significance (Apr 23, 2019)link
3-23917960-C-T not specified Uncertain significance (Jun 23, 2022)link
3-23917962-G-A Uncertain significance (Jun 11, 2019)link
3-23917979-C-T Likely benign (Oct 21, 2022)link
3-23917983-C-T Uncertain significance (Mar 24, 2022)link
3-23917986-AC-A Diamond-Blackfan anemia 12 Pathogenic (Aug 30, 2021)link
3-23917987-C-T Uncertain significance (Nov 19, 2021)link
3-23917997-T-G Uncertain significance (Mar 18, 2022)link
3-23918004-C-T Uncertain significance (Aug 24, 2021)link
3-23918015-C-T Likely benign (Mar 12, 2022)link
3-23918025-A-G Uncertain significance (Aug 29, 2022)link
3-23918027-G-A Likely benign (Jul 08, 2021)link
3-23918036-G-A Diamond-Blackfan anemia 12 Conflicting interpretations of pathogenicity (Oct 26, 2022)link
3-23918038-G-A Likely benign (Dec 09, 2021)link
3-23918046-G-A Likely benign (Feb 18, 2021)link

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RPL15protein_codingprotein_codingENST00000307839 37148
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9710.028500000.00
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.83701290.5450.000007641302
Missense in Polyphen522.4680.22254311
Synonymous-2.005841.61.390.00000192425
Loss of Function3.07011.00.007.39e-795

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

Disease
DISEASE: Diamond-Blackfan anemia 12 (DBA12) [MIM:615550]: 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:23812780}. 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 (Consensus)

Recessive Scores

pRec
0.171

Intolerance Scores

loftool
rvis_EVS
-0.08
rvis_percentile_EVS
47.79

Haploinsufficiency Scores

pHI
0.481
hipred
Y
hipred_score
0.783
ghis
0.662

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
S
essential_gene_gene_trap
E
gene_indispensability_pred
E
gene_indispensability_score
0.860

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Rpl15
Phenotype

Gene ontology

Biological process
nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;cytoplasmic translation;translation;translational initiation;SRP-dependent cotranslational protein targeting to membrane
Cellular component
nucleus;cytosol;ribosome;membrane;cytosolic large ribosomal subunit
Molecular function
RNA binding;structural constituent of ribosome;protein binding;cadherin binding