RPS15

ribosomal protein S15, the group of S ribosomal proteins

Basic information

Region (hg38): 19:1438357-1440495

Links

ENSG00000115268 ∙ NCBI:6209 ∙ OMIM:180535 ∙ HGNC:10388 ∙ Uniprot:P62841 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RPS15 gene.

• not provided (3 variants)
• not specified (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPS15 gene is commonly pathogenic or not.

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

Variants in RPS15

This is a list of pathogenic ClinVar variants found in the RPS15 region.

Position	Type	Phenotype	Significance	ClinVar
19-1438866-C-T		not specified	Benign (May 04, 2021)
19-1440069-G-C		not specified	Benign (May 04, 2021)
19-1440087-A-C		Inborn genetic diseases	Uncertain significance (Jan 18, 2023)
19-1440375-C-T			Benign (Jul 04, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RPS15	protein_coding	protein_coding	ENST00000586686	4	2226

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.833	0.164	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.78	46	94.8	0.485	0.00000707	916
Missense in Polyphen		3	10.411	0.28814		149
Synonymous	-3.10	66	40.8	1.62	0.00000289	283
Loss of Function	2.25	0	5.89	0.00	2.54e-7	74

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: 0.185

Intolerance Scores

• rvis_EVS: 0.01
• rvis_percentile_EVS: 54.63

Haploinsufficiency Scores

• pHI: 0.161
• hipred: N
• hipred_score: 0.483
• ghis: 0.623

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.824

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rps15

Zebrafish Information Network

• Gene name: rps15
• Affected structure: post-vent region
• Phenotype tag: abnormal
• Phenotype quality: morphology

Gene ontology

• Biological process: ribosomal small subunit assembly;ribosomal small subunit export from nucleus;nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;osteoblast differentiation;rRNA processing;translation;translational initiation;SRP-dependent cotranslational protein targeting to membrane;ribosomal small subunit biogenesis
• Cellular component: nucleus;nucleoplasm;cytosol;focal adhesion;membrane;cytosolic small ribosomal subunit
• Molecular function: DNA binding;RNA binding;structural constituent of ribosome;protein binding