GeneBe

RPL15

protein-coding

ribosomal protein L15, the group of L ribosomal proteins

Gene summary

Ribosomes, the organelles that catalyze protein synthesis, consist of a small 40S subunit and a large 60S subunit. Together these subunits are composed of four RNA species and approximately 80 structurally distinct proteins. This gene encodes a member of the L15E family of ribosomal proteins and a component of the 60S subunit. This gene shares sequence similarity with the yeast ribosomal protein YL10 gene. Elevated expression of this gene has been observed in esophageal tumors and gastric cancer tissues, and deletion of this gene has been observed in a Diamond-Blackfan anemia (DBA) patient. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. [provided by RefSeq, Mar 2017]

MANE transcript

NM_002948.5

Inheritance

AD

ClinVar variants

P:13U:79B:52

Top phenotype

Diamond-Blackfan anemia 12

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr3:23,916,591-23,924,374

External References & Databases

Ensembl (ENSG00000174748)NCBI Gene (6138)OMIM (604174)HGNC:10306GenCCUniProt (P61313)AlphaFoldClinVar (RPL15)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~7.8 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

Diamond-Blackfan anemia 12STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0014245

Submitter: Labcorp Genetics (formerly Invitae)

Diamond-Blackfan anemiaSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0015253

Submitter: Orphanet

Diamond-Blackfan anemia 12STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0014245

Submitter: PanelApp Australia

Clinical Genomic Database (CGD)

Diamond-Blackfan anemia 12AD

Manifestation: Cardiovascular; Hematologic; Musculoskeletal; Neurologic; Oncologic

Intervention: Cardiovascular; Hematologic; Oncologic

Rationale: 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

Refs: 20301769; 23812780Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to RPL15 variants in ClinVar

4 Conditions Cataloged
not providedTotal: 137
not specifiedTotal: 29
Diamond-Blackfan anemia 12Total: 17
RPL15-related disorderTotal: 11

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_002948.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
3
clinvar
45
clinvar
5
clinvar
 53
missense
2
clinvar
1
clinvar
74
clinvar
2
clinvar
 79
nonsense
4
clinvar
1
clinvar
 5
start loss
0
frameshift
3
clinvar
1
clinvar
 4
splice donor/acceptor (+/-2bp)
2
clinvar
1
clinvar
 3
Total11279475144

Highest pathogenic variant AF is 0.0000041367216

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 81 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_002948.5RefSeqNP_002939.23MANE Select
ENST00000307839.10EnsemblENSP00000309334.53MANE Select
NM_001253379.2RefSeqNP_001240308.13Standard
NM_001253380.2RefSeqNP_001240309.13Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Ribosome - Homo sapiens (human)
  • Cytoplasmic Ribosomal Proteins
  • SRP-dependent cotranslational protein targeting to membrane
  • Eukaryotic Translation Initiation
  • Eukaryotic Translation Termination

Biological Process

  • nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
  • cytoplasmic translation
  • translation
  • translational initiation
  • SRP-dependent cotranslational protein targeting to membrane

Molecular Function

  • RNA binding
  • structural constituent of ribosome
  • protein binding
  • cadherin binding

Cellular Component

  • nucleus
  • cytosol
  • ribosome
  • membrane
  • cytosolic large ribosomal subunit

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000307839
Coding exons
3
Length
7148
Individuals with no LoFs
0
Homozygous LoFs
0
Heterozygous LoFs
0
Defined
0
p
0.00
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense1.83701290.5450.000007641302
Missense (PolyPhen)522.4680.22254311
Synonymous-2.005841.61.390.00000192425
Loss of Function3.07011.00.007.39e-795

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American00.0absent
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish00.0absent
European (Non-Finnish)00.0absent
South Asian00.0absent
Other00.0absent

dbNSFP Gene Annotations

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.;

Recessive Scores

pRec
0.171

Intolerance Scores

RVIS EVS
-0.08
RVIS percentile EVS
47.79

Essentials

Essential (CRISPR)
E
Essential (CRISPR2)
S
Essential (gene trap)
E
Indispensability pred.
E
Indispensability score
0.860

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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