RPS25

ribosomal protein S25, the group of S ribosomal proteins

Basic information

Region (hg38): 11:119015711-119018691

Links

ENSG00000118181 ∙ NCBI:6230 ∙ OMIM:180465 ∙ HGNC:10413 ∙ Uniprot:P62851 ∙ 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 RPS25 gene.

• not provided (11 variants)
• Inborn genetic diseases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPS25 gene is commonly pathogenic or not.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			1			1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice variant						0
non coding					10	10
Total	0	0	1	0	11

Variants in RPS25

This is a list of pathogenic ClinVar variants found in the RPS25 region.

Position	Type	Phenotype	Significance	ClinVar
11-119015870-G-C		Inborn genetic diseases	Uncertain significance (Jul 13, 2021)
11-119015893-G-A			Benign (Jun 21, 2018)
11-119018306-G-A			Benign (May 26, 2021)
11-119018318-G-A			Benign (May 16, 2021)
11-119018363-G-T			Benign (May 15, 2021)
11-119018404-A-G			Benign (May 15, 2021)
11-119018422-A-G			Benign (May 15, 2021)
11-119018475-T-C			Benign (May 15, 2021)
11-119018537-A-AG			Benign (May 15, 2021)
11-119018668-G-A			Benign (May 15, 2021)
11-119018686-G-GAGA			Benign (May 30, 2021)
11-119018686-G-GAGGAGA			Benign (May 15, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RPS25	protein_coding	protein_coding	ENST00000527673	4	2980

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.863	0.135	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.83	23	64.2	0.358	0.00000277	807
Missense in Polyphen		7	15.045	0.46526		224
Synonymous	-1.16	32	24.7	1.30	0.00000108	244
Loss of Function	2.37	0	6.52	0.00	3.15e-7	91

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: 0.171

Intolerance Scores

• rvis_EVS: 0.01
• rvis_percentile_EVS: 54.63

Haploinsufficiency Scores

• pHI: 0.943
• hipred: Y
• hipred_score: 0.526
• ghis: 0.659

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	Medium	Low	Medium
Cancer	Low	Low	Low

Mouse Genome Informatics

• Gene name: Rps25

Gene ontology

• Biological process: nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;translation;translational initiation;SRP-dependent cotranslational protein targeting to membrane
• Cellular component: nucleus;nucleoplasm;nucleolus;cytosol;ribosome;postsynaptic density;small ribosomal subunit;cytosolic small ribosomal subunit;extracellular exosome
• Molecular function: RNA binding;protein binding