RPL15

ribosomal protein L15, the group of L ribosomal proteins

Basic information

Region (hg38): 3:23916591-23924374

Links

ENSG00000174748 ∙ NCBI:6138 ∙ OMIM:604174 ∙ HGNC:10306 ∙ Uniprot:P61313 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Diamond-Blackfan anemia 12	AD	Cardiovascular; Hematologic; Oncologic	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	Cardiovascular; Hematologic; Musculoskeletal; Neurologic; Oncologic	20301769; 23812780

ClinVar

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

• not provided (3 variants)
• Diamond-Blackfan anemia 12 (2 variants)
• RPL15-related disorder (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			1	33	6	40
missense		1	50	2	1	54
nonsense	2					2
start loss						0
frameshift	1				1	2
inframe indel						0
splice donor/acceptor (+/-2bp)	2					2
splice region			1	5	4	10
non coding			2	10	8	20
Total	5	1	53	45	16

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)
3-23917766-T-C			Likely benign (Aug 09, 2018)
3-23917859-G-C		not specified	Uncertain significance (Jan 03, 2019)
3-23917877-C-T		RPL15-related disorder	Likely benign (Sep 20, 2023)
3-23917882-A-C			Uncertain significance (May 18, 2023)
3-23917888-T-C		Diamond-Blackfan anemia 12	Pathogenic (May 18, 2023)
3-23917904-G-A			Likely benign (Jun 06, 2023)
3-23917906-C-G			Uncertain significance (Sep 19, 2022)
3-23917907-T-A			Likely benign (Jul 26, 2023)
3-23917914-A-G			Uncertain significance (Jul 19, 2022)
3-23917934-C-G		not specified • RPL15-related disorder	Benign/Likely benign (Jan 29, 2024)
3-23917934-C-T			Likely benign (Nov 20, 2023)
3-23917944-C-A			Uncertain significance (Jun 30, 2022)
3-23917944-C-T		Diamond-Blackfan anemia 12	Pathogenic (May 18, 2023)
3-23917946-G-T			Uncertain significance (Apr 23, 2019)
3-23917960-C-T		not specified	Uncertain significance (Jun 23, 2022)
3-23917962-G-A			Uncertain significance (Feb 06, 2023)
3-23917977-C-T		not specified	Uncertain significance (Jan 17, 2024)
3-23917979-C-T			Likely benign (Apr 16, 2023)
3-23917981-G-T			Uncertain significance (Dec 10, 2022)
3-23917983-C-T			Uncertain significance (Mar 24, 2022)
3-23917986-AC-A		Diamond-Blackfan anemia 12	Pathogenic (Aug 30, 2021)
3-23917987-C-T			Uncertain significance (Nov 19, 2021)
3-23917997-T-G			Uncertain significance (Jul 26, 2023)
3-23918004-C-T			Uncertain significance (Mar 08, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RPL15	protein_coding	protein_coding	ENST00000307839	3	7148

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.971	0.0285	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.83	70	129	0.545	0.00000764	1302
Missense in Polyphen		5	22.468	0.22254		311
Synonymous	-2.00	58	41.6	1.39	0.00000192	425
Loss of Function	3.07	0	11.0	0.00	7.39e-7	95

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

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

• 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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Rpl15

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