RPS19

ribosomal protein S19, the group of S ribosomal proteins|MicroRNA protein coding host genes

Basic information

Region (hg38): 19:41860255-41872925

Previous symbols: [ "LOH19CR1" ]

Links

ENSG00000105372 ∙ NCBI:6223 ∙ OMIM:603474 ∙ HGNC:10402 ∙ Uniprot:P39019 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Diamond-Blackfan anemia 1 (Definitive), mode of inheritance: AD
• Diamond-Blackfan anemia (Supportive), mode of inheritance: AD
• Diamond-Blackfan anemia 1 (Definitive), mode of inheritance: AD
• Diamond-Blackfan anemia 1 (Strong), mode of inheritance: AD
• Diamond-Blackfan anemia (Definitive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Diamond-Blackfan anemia 1	AD	Cardiovascular; Hematologic; Oncologic	Specific treatment of anemia (eg, steroids, regular transfusions) can be effective; Surveillance for and early treatment of malignancy may allow early detection and management; Individuals with DBA may manifest a variety of congenital malformations (eg, cardiac anomalies), and awareness may allow prompt detection and management	Cardiovascular; Craniofacial; Hematologic; Musculoskeletal; Neurologic; Oncologic; Ophthalmologic; Renal	13722603; 16317735; 276838; 273451; 1958491; 8826887; 9988267; 10541318; 10590074; 16741228; 19061985; 20301769; 23812780; 23812780

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RPS19 gene.

• Diamond-Blackfan anemia (34 variants)
• not provided (12 variants)
• Diamond-Blackfan anemia 1 (9 variants)
• RPS19-related disorder (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPS19 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			4	34		38
missense	6	13	39			58
nonsense	10	1	1			12
start loss	3		1			4
frameshift	20	2	2			24
inframe indel		1	1			2
splice donor/acceptor (+/-2bp)	5	5				10
splice region	1		10	3	1	15
non coding			8	28	9	45
Total	44	22	56	62	9

Variants in RPS19

This is a list of pathogenic ClinVar variants found in the RPS19 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-41860257-C-T			Uncertain significance (Dec 05, 2022)
19-41860264-C-T		Diamond-Blackfan anemia 1	Uncertain significance (Jan 13, 2018)
19-41860280-A-G		Diamond-Blackfan anemia 1	Likely benign (Jan 13, 2018)
19-41860303-C-T		Diamond-Blackfan anemia 1	Uncertain significance (Jan 12, 2018)
19-41860315-G-T		Diamond-Blackfan anemia	Benign (May 01, 2023)
19-41860325-C-C		not specified	Benign (Aug 08, 2016)
19-41860383-C-G			Benign (Mar 03, 2015)
19-41860761-A-G		Diamond-Blackfan anemia 1	Likely benign (Aug 22, 2021)
19-41860762-C-T		Diamond-Blackfan anemia 1	Benign/Likely benign (Sep 14, 2021)
19-41860766-C-A		Diamond-Blackfan anemia 1	Likely benign (Jan 12, 2018)
19-41860766-C-T		Diamond-Blackfan anemia 1 • not specified	Uncertain significance (Mar 02, 2021)
19-41860768-C-T		not specified • Diamond-Blackfan anemia 1	Conflicting classifications of pathogenicity (Jan 12, 2018)
19-41860775-A-C		Diamond-Blackfan anemia	Pathogenic (Oct 22, 2023)
19-41860775-A-G		Diamond-Blackfan anemia 1	Uncertain significance (May 22, 2022)
19-41860777-G-A		Diamond-Blackfan anemia	Pathogenic (Jul 29, 2022)
19-41860777-G-C		Diamond-Blackfan anemia	Pathogenic (Aug 04, 2016)
19-41860777-G-T		Diamond-Blackfan anemia • Diamond-Blackfan anemia 1	Pathogenic (Feb 04, 2023)
19-41860780-T-G		Diamond-Blackfan anemia	Likely benign (Apr 22, 2023)
19-41860784-G-T		Diamond-Blackfan anemia	Uncertain significance (Aug 28, 2021)
19-41860786-T-TA		Diamond-Blackfan anemia	Pathogenic (Dec 16, 2019)
19-41860787-AC-A		Diamond-Blackfan anemia 1	Likely pathogenic (-)
19-41860789-T-A		Diamond-Blackfan anemia	Likely benign (Aug 10, 2020)
19-41860789-TG-T		Diamond-Blackfan anemia	Pathogenic (Oct 11, 2019)
19-41860791-TA-T		Diamond-Blackfan anemia	Pathogenic (Jun 09, 2017)
19-41860794-AAG-CTCCAGCATCCAGTT		not specified	Uncertain significance (Aug 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RPS19	protein_coding	protein_coding	ENST00000598742	5	13007

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.921	0.0785	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.45	53	92.2	0.575	0.00000596	926
Missense in Polyphen		2	14.212	0.14073		185
Synonymous	-2.13	54	37.4	1.44	0.00000238	297
Loss of Function	2.64	0	8.14	0.00	3.90e-7	88

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: Required for pre-rRNA processing and maturation of 40S ribosomal subunits. {ECO:0000269|PubMed:16990592}.
• Pathway: Ribosome - Homo sapiens (human);Human Complement System;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: 0.400

Intolerance Scores

• rvis_EVS: -0.21
• rvis_percentile_EVS: 38.28

Haploinsufficiency Scores

• pHI: 0.676
• hipred: Y
• hipred_score: 0.771
• ghis: 0.554

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.960

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rps19
• Phenotype: limbs/digits/tail phenotype; pigmentation 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); integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: rps19
• Affected structure: erythroid lineage cell
• Phenotype tag: abnormal
• Phenotype quality: absent

Gene ontology

• Biological process: ribosomal small subunit assembly;nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA);monocyte chemotaxis;rRNA processing;translation;translational initiation;SRP-dependent cotranslational protein targeting to membrane;nucleolus organization;response to extracellular stimulus;erythrocyte differentiation;maturation of SSU-rRNA;killing of cells of other organism;ribosomal small subunit biogenesis;defense response to Gram-negative bacterium;protein tetramerization;positive regulation of cellular component movement;positive regulation of respiratory burst involved in inflammatory response;negative regulation of respiratory burst involved in inflammatory response;antimicrobial humoral immune response mediated by antimicrobial peptide
• Cellular component: nucleoplasm;nucleolus;cytoplasm;cytosol;ribosome;focal adhesion;postsynaptic density;membrane;cytosolic small ribosomal subunit;extracellular exosome
• Molecular function: RNA binding;structural constituent of ribosome;protein binding;fibroblast growth factor binding;protein kinase binding;protein homodimerization activity