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

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

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.

• not provided (8 variants)
• Diamond-Blackfan anemia 20 (1 variants)

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				3		3
missense			1			1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice variant	1			1		2
non coding				1	2	3
Total	1	0	1	5	2

Variants in RPS15A

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

Position	Type	Phenotype	Significance	ClinVar
16-18784831-A-G			Likely benign (Sep 21, 2022)
16-18784832-T-TAAC			Likely benign (May 11, 2022)
16-18788063-C-T		Diamond-Blackfan anemia 20	Pathogenic (Apr 06, 2021)
16-18788093-A-T			Likely benign (Apr 06, 2022)
16-18788132-G-A			Likely benign (Oct 11, 2022)
16-18788293-C-A			Benign (May 14, 2021)
16-18789063-G-T			Likely benign (Aug 03, 2022)
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