RPS13

ribosomal protein S13, the group of S ribosomal proteins|Small nucleolar RNA protein coding host genes

Basic information

Region (hg38): 11:17074387-17077715

Links

ENSG00000110700 ∙ NCBI:6207 ∙ OMIM:180476 ∙ HGNC:10386 ∙ Uniprot:P62277 ∙ 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 RPS13 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPS13 gene is commonly pathogenic or not.

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

Variants in RPS13

This is a list of pathogenic ClinVar variants found in the RPS13 region.

Position	Type	Phenotype	Significance	ClinVar
11-17075542-T-C		Inborn genetic diseases	Uncertain significance (Apr 25, 2023)
11-17077484-A-G			Likely benign (Dec 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RPS13	protein_coding	protein_coding	ENST00000525634	6	3399

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.876	0.123	124555	0	1	124556	0.00000401

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.77	39	84.8	0.460	0.00000458	953
Missense in Polyphen		5	17.831	0.28041		248
Synonymous	-1.29	38	29.1	1.30	0.00000134	310
Loss of Function	2.83	1	11.2	0.0892	6.87e-7	118

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)	0.00000886	0.00000887
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;TNFalpha;Peptide chain elongation;Eukaryotic Translation Elongation;GTP hydrolysis and joining of the 60S ribosomal subunit;Cap-dependent Translation Initiation (Consensus)

Recessive Scores

• pRec: 0.270

Intolerance Scores

• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.04

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.802
• ghis: 0.633

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• 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: Rps13

Gene ontology

• Biological process: nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;translation;translational initiation;SRP-dependent cotranslational protein targeting to membrane;negative regulation of RNA splicing
• Cellular component: nucleus;nucleoplasm;nucleolus;cytosol;ribosome;focal adhesion;postsynaptic density;membrane;cytosolic small ribosomal subunit;extracellular exosome
• Molecular function: RNA binding;mRNA binding;structural constituent of ribosome;protein binding;mRNA 5'-UTR binding;small ribosomal subunit rRNA binding