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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:P61313AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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 (95 variants)
  • not specified (7 variants)
  • Diamond-Blackfan anemia 12 (5 variants)
  • Inborn genetic diseases (4 variants)
  • RPL15-related condition (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.

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
2
clinvar
25
clinvar
5
clinvar
32
missense
1
clinvar
40
clinvar
1
clinvar
42
nonsense
1
clinvar
1
start loss
0
frameshift
1
clinvar
1
clinvar
2
inframe indel
0
splice donor/acceptor (+/-2bp)
2
clinvar
2
splice region
3
3
6
non coding
2
clinvar
7
clinvar
8
clinvar
17
Total 4 1 44 32 15

Variants in RPL15

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

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

Position Type Phenotype Significance ClinVar
3-23917732-A-C Likely benign (Dec 21, 2018)1194728
3-23917766-T-C Likely benign (Aug 09, 2018)1199763
3-23917859-G-C not specified Uncertain significance (Jan 03, 2019)1336971
3-23917877-C-T RPL15-related condition Likely benign (Sep 20, 2023)1107700
3-23917882-A-C Uncertain significance (May 18, 2023)2662347
3-23917888-T-C Diamond-Blackfan anemia 12 Pathogenic (May 18, 2023)2502337
3-23917904-G-A Likely benign (Jun 06, 2023)2886650
3-23917906-C-G Uncertain significance (Sep 19, 2022)2183188
3-23917907-T-A Likely benign (Jul 26, 2023)2747016
3-23917914-A-G Uncertain significance (Jul 19, 2022)1368290
3-23917934-C-G not specified • RPL15-related condition Benign (Jan 29, 2024)436551
3-23917934-C-T Likely benign (Nov 20, 2023)2884137
3-23917944-C-A Uncertain significance (Jun 30, 2022)2417517
3-23917944-C-T Diamond-Blackfan anemia 12 Pathogenic (May 18, 2023)2502336
3-23917946-G-T Uncertain significance (Apr 23, 2019)1305196
3-23917960-C-T not specified Uncertain significance (Jun 23, 2022)2443245
3-23917962-G-A Uncertain significance (Feb 06, 2023)1306432
3-23917977-C-T not specified Uncertain significance (Jan 17, 2024)3156040
3-23917979-C-T Likely benign (Apr 16, 2023)1985307
3-23917981-G-T Uncertain significance (Dec 10, 2022)2787257
3-23917983-C-T Uncertain significance (Mar 24, 2022)1979895
3-23917986-AC-A Diamond-Blackfan anemia 12 Pathogenic (Aug 30, 2021)1709989
3-23917987-C-T Uncertain significance (Nov 19, 2021)1400084
3-23917997-T-G Uncertain significance (Jul 26, 2023)2171701
3-23918004-C-T Uncertain significance (Mar 08, 2021)1477433

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