RPS3A

ribosomal protein S3A, the group of Small nucleolar RNA protein coding host genes|S ribosomal proteins

Basic information

Region (hg38): 4:151099623-151104642

Previous symbols: [ "MFTL" ]

Links

ENSG00000145425 ∙ NCBI:6189 ∙ OMIM:180478 ∙ HGNC:10421 ∙ Uniprot:P61247 ∙ 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 RPS3A gene.

• Inborn genetic diseases (3 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPS3A gene is commonly pathogenic or not.

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

Variants in RPS3A

This is a list of pathogenic ClinVar variants found in the RPS3A region.

Position	Type	Phenotype	Significance	ClinVar
4-151100479-A-T			Benign (Jun 13, 2018)
4-151102889-G-A		Inborn genetic diseases	Uncertain significance (Nov 22, 2021)
4-151102899-A-G		Inborn genetic diseases	Uncertain significance (Dec 28, 2022)
4-151104535-C-A		Inborn genetic diseases	Uncertain significance (Sep 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RPS3A	protein_coding	protein_coding	ENST00000274065	6	5080

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.970	0.0299	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.23	68	143	0.476	0.00000759	1757
Missense in Polyphen		2	13.213	0.15137		242
Synonymous	-2.61	68	45.6	1.49	0.00000222	475
Loss of Function	3.05	0	10.9	0.00	5.40e-7	149

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

• Function: FUNCTION: May play a role during erythropoiesis through regulation of transcription factor DDIT3. {ECO:0000255|HAMAP-Rule:MF_03122}.
• 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: 0.302

Intolerance Scores

• rvis_EVS: 0.01
• rvis_percentile_EVS: 54.63

Haploinsufficiency Scores

• pHI: 0.997
• hipred: Y
• hipred_score: 0.809
• ghis: 0.654

Essentials

• essential_gene_CRISPR: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.948

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rps3a1

Zebrafish Information Network

• Gene name: rps3a
• Affected structure: post-vent region
• Phenotype tag: abnormal
• Phenotype quality: bent

Gene ontology

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