RPS15A

ribosomal protein S15a, the group of S ribosomal proteins

Basic information

Region (hg38): 16:18781294-18790383

Links

ENSG00000134419 ∙ NCBI:6210 ∙ OMIM:603674 ∙ HGNC:10389 ∙ Uniprot:P62244 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Diamond-Blackfan anemia 20 (Limited), mode of inheritance: AD
• Diamond-Blackfan anemia (Supportive), mode of inheritance: AD
• Diamond-Blackfan anemia 20 (Limited), mode of inheritance: AD
• Diamond-Blackfan anemia 20 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Diamond-Blackfan anemia 20	AD	Hematologic; Oncologic	Specific treatment of anemia (eg, steroids, regular transfusions) can be effective; Surveillance for and early treatment of malignancy may be beneficial	Hematologic; Oncologic	28280134

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RPS15A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPS15A 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				9		9
missense			2			2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding				4	2	6
Total	0	0	2	13	2

Variants in RPS15A

This is a list of pathogenic ClinVar variants found in the RPS15A region.

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

Position	Type	Phenotype	Significance	ClinVar
16-18784797-G-A			Likely benign (Dec 12, 2023)
16-18784831-A-G			Likely benign (Nov 22, 2023)
16-18784832-TAAC-T			Likely benign (Oct 20, 2023)
16-18784832-TAACAAC-T			Likely benign (Dec 21, 2023)
16-18784832-T-TAAC			Likely benign (Jan 24, 2023)
16-18788063-C-T		Diamond-Blackfan anemia 20	Pathogenic (Apr 06, 2021)
16-18788093-A-T			Likely benign (Nov 24, 2023)
16-18788132-G-A			Likely benign (Oct 11, 2022)
16-18788293-C-A			Benign (May 14, 2021)
16-18788967-G-A			Likely benign (Jun 21, 2023)
16-18788994-C-G			Likely benign (Dec 31, 2023)
16-18789000-G-A			Likely benign (Aug 01, 2023)
16-18789006-C-G			Likely benign (Mar 18, 2023)
16-18789008-G-T			Likely benign (Sep 08, 2023)
16-18789009-G-C			Likely benign (Aug 28, 2023)
16-18789053-C-T			Uncertain significance (Jan 14, 2023)
16-18789063-G-T			Likely benign (Oct 29, 2023)
16-18789100-T-C			Uncertain significance (May 13, 2022)
16-18789316-G-C			Benign (May 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RPS15A	protein_coding	protein_coding	ENST00000322989	4	9089

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.802	0.193	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.24	20	74.2	0.270	0.00000392	859
Missense in Polyphen		1	6.9854	0.14316		113
Synonymous	-0.744	33	28.0	1.18	0.00000156	246
Loss of Function	2.14	0	5.36	0.00	2.26e-7	66

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

• Pathway: Ribosome - Homo sapiens (human);Cytoplasmic Ribosomal Proteins;SRP-dependent cotranslational protein targeting to membrane;Formation of the ternary complex, and subsequently, the 43S complex;Translation initiation complex formation;Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S;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);Ribosomal scanning and start codon recognition;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: 0.230

Intolerance Scores

• rvis_EVS: 0.06
• rvis_percentile_EVS: 58

Haploinsufficiency Scores

• pHI: 0.373
• hipred: Y
• hipred_score: 0.748
• ghis: 0.580

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.973

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low

Mouse Genome Informatics

• Gene name: Rps15a

Zebrafish Information Network

• Gene name: rps15a
• Affected structure: nucleate erythrocyte
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;translation;translational initiation;SRP-dependent cotranslational protein targeting to membrane;positive regulation of cell population proliferation;response to virus;positive regulation of cell cycle
• Cellular component: nucleoplasm;cytoplasm;cytosol;membrane;cytosolic small ribosomal subunit;extracellular exosome
• Molecular function: RNA binding;structural constituent of ribosome;protein binding