RPSA

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

Basic information

Region (hg38): 3:39406716-39426255

Previous symbols: [ "LAMR1" ]

Links

ENSG00000168028 ∙ NCBI:3921 ∙ OMIM:150370 ∙ HGNC:6502 ∙ Uniprot:P08865 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• familial isolated congenital asplenia (Supportive), mode of inheritance: AD
• familial isolated congenital asplenia (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Asplenia, isolated congenital	AD	Allergy/Immunology/Infectious	Individuals are susceptible to severe bacterial infections in early life, and awareness may allow prophylaxis and early and aggressive management of infections	Allergy/Immunology/Infectious; Gastrointestinal	20846672; 23579497

ClinVar

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

• not provided (1 variants)
• Familial isolated congenital asplenia (1 variants)

Variants pathogenicity by type

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

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				21	2	23
missense	1	1	33			35
nonsense						0
start loss						0
frameshift				2		2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			7	5		12
non coding				19	5	24
Total	1	1	33	42	7

Variants in RPSA

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

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
3-39407646-T-C		not specified • Familial isolated congenital asplenia	Benign (Nov 07, 2021)
3-39407675-C-T			Likely benign (Jul 19, 2022)
3-39407678-C-T		Familial isolated congenital asplenia	Pathogenic (May 24, 2013)
3-39407686-G-A			Likely benign (Jul 10, 2023)
3-39407707-C-T			Likely benign (Nov 25, 2023)
3-39407734-C-T			Likely benign (May 17, 2022)
3-39407736-C-T			Uncertain significance (Sep 07, 2023)
3-39407753-A-G			Uncertain significance (Oct 18, 2017)
3-39407756-G-A			Uncertain significance (Dec 16, 2023)
3-39407761-G-C			Uncertain significance (Jun 22, 2022)
3-39407794-A-G			Uncertain significance (Jan 12, 2024)
3-39408574-C-T		Familial isolated congenital asplenia	Benign (Nov 07, 2021)
3-39408588-C-T			Likely benign (May 22, 2023)
3-39408592-C-T			Likely benign (Sep 07, 2022)
3-39408594-G-C			Likely benign (Jun 04, 2023)
3-39408599-C-T			Likely benign (Feb 07, 2022)
3-39408627-A-G		not specified	Uncertain significance (May 29, 2024)
3-39408633-C-A		Familial isolated congenital asplenia	Pathogenic (May 24, 2013)
3-39408633-C-G			Uncertain significance (Oct 26, 2020)
3-39408644-C-T		Familial isolated congenital asplenia	Pathogenic (May 24, 2013)
3-39408649-G-C			Likely benign (Jul 06, 2022)
3-39408655-A-C			Likely benign (Jul 17, 2023)
3-39408657-C-G			Uncertain significance (Jul 24, 2022)
3-39408661-T-A			Likely benign (Aug 15, 2022)
3-39408662-G-A			Uncertain significance (Apr 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RPSA	protein_coding	protein_coding	ENST00000301821	6	5854

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.930	0.0696	123271	0	1	123272	0.00000406

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.42	80	168	0.475	0.00000942	1911
Missense in Polyphen		3	25.011	0.11995		381
Synonymous	0.0943	56	56.9	0.984	0.00000297	598
Loss of Function	3.07	1	12.9	0.0776	5.55e-7	148

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	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for the assembly and/or stability of the 40S ribosomal subunit. Required for the processing of the 20S rRNA- precursor to mature 18S rRNA in a late step of the maturation of 40S ribosomal subunits. Also functions as a cell surface receptor for laminin. Plays a role in cell adhesion to the basement membrane and in the consequent activation of signaling transduction pathways. May play a role in cell fate determination and tissue morphogenesis. Acts as a PPP1R16B-dependent substrate of PPP1CA. {ECO:0000255|HAMAP-Rule:MF_03016, ECO:0000269|PubMed:16263087, ECO:0000269|PubMed:6300843}.; FUNCTION: (Microbial infection) Acts as a receptor for the Dengue virus. {ECO:0000269|PubMed:15507651}.; FUNCTION: (Microbial infection) Acts as a receptor for the Venezuelan equine encephalitis virus. {ECO:0000269|PubMed:1385835}.; FUNCTION: (Microbial infection) Acts as a receptor for bacteria. {ECO:0000269|PubMed:15516338}.
• Disease: DISEASE: Asplenia, isolated congenital (ICAS) [MIM:271400]: A rare primary immunodeficiency and life-threatening condition, often presenting with pneumococcal sepsis. Most affected individuals die of severe bacterial infections in early childhood. Isolated asplenia is distinct from asplenia associated with other complex visceral defects, notably heterotaxy syndromes such as Ivemark syndrome. {ECO:0000269|PubMed:23579497}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Ribosome - Homo sapiens (human);Cytoplasmic Ribosomal Proteins;prion pathway;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;Alpha6Beta4Integrin;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: 0.288

Intolerance Scores

• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.25

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.681
• ghis: 0.656

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.933

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rpsa
• Phenotype: endocrine/exocrine gland phenotype; growth/size/body region phenotype; craniofacial phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: rpsa
• Affected structure: trunk
• Phenotype tag: abnormal
• Phenotype quality: necrotic

Gene ontology

• Biological process: ribosomal small subunit assembly;nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA);endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA);rRNA export from nucleus;translation;translational initiation;SRP-dependent cotranslational protein targeting to membrane;cell adhesion;viral entry into host cell
• Cellular component: nucleus;nucleoplasm;cytoplasm;cytosol;plasma membrane;membrane;cytosolic small ribosomal subunit;extracellular exosome
• Molecular function: virus receptor activity;RNA binding;structural constituent of ribosome;laminin receptor activity;protein binding;ribosome binding;laminin binding