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GeneBe

RPS19

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

Basic information

Region (hg38): 19:41860254-41872925

Previous symbols: [ "LOH19CR1" ]

Links

ENSG00000105372NCBI:6223OMIM:603474HGNC:10402Uniprot:P39019AlphaFoldGenCCjaxSfariGnomADPubmed

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

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Diamond-Blackfan anemia 1ADCardiovascular; Hematologic; OncologicSpecific 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 managementCardiovascular; Craniofacial; Hematologic; Musculoskeletal; Neurologic; Oncologic; Ophthalmologic; Renal13722603; 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 (131 variants)
  • Diamond-Blackfan anemia 1 (45 variants)
  • not provided (38 variants)
  • not specified (12 variants)
  • - (2 variants)
  • Landsteiner-Wiener phenotype (1 variants)
  • Hepatoblastoma (1 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.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous 1 22 23
missense 5 12 29 7 53
nonsense 13 1 2 1 17
start loss 0
frameshift 22 1 23
inframe indel 1 1
splice variant 3 6 6 6 2 23
non coding 8 23 7 38
Total 43 21 46 59 9

Variants in RPS19

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

Position Type Phenotype Significance ClinVar
19-41860264-C-T Diamond-Blackfan anemia 1 Uncertain significance (Jan 13, 2018)link
19-41860280-A-G Diamond-Blackfan anemia 1 Likely benign (Jan 13, 2018)link
19-41860303-C-T Diamond-Blackfan anemia 1 Uncertain significance (Jan 12, 2018)link
19-41860315-G-T Diamond-Blackfan anemia Benign (May 01, 2023)link
19-41860325-C-C not specified Benign (Aug 08, 2016)link
19-41860383-C-G Benign (Mar 03, 2015)link
19-41860761-A-G Diamond-Blackfan anemia 1 Likely benign (Aug 22, 2021)link
19-41860762-C-T Diamond-Blackfan anemia 1 Benign/Likely benign (Sep 14, 2021)link
19-41860766-C-A Diamond-Blackfan anemia 1 Likely benign (Jan 12, 2018)link
19-41860766-C-T Diamond-Blackfan anemia 1 • not specified Uncertain significance (Mar 02, 2021)link
19-41860768-C-T not specified • Diamond-Blackfan anemia 1 Conflicting interpretations of pathogenicity (Jan 12, 2018)link
19-41860775-A-G Diamond-Blackfan anemia 1 Uncertain significance (May 22, 2022)link
19-41860777-G-A Diamond-Blackfan anemia Pathogenic (Jul 29, 2022)link
19-41860777-G-C Diamond-Blackfan anemia Pathogenic (Aug 04, 2016)link
19-41860777-G-T Diamond-Blackfan anemia • Diamond-Blackfan anemia 1 Pathogenic (Aug 01, 2022)link
19-41860780-T-G Diamond-Blackfan anemia Likely benign (Apr 22, 2023)link
19-41860784-G-T Diamond-Blackfan anemia Uncertain significance (Aug 28, 2021)link
19-41860786-T-TA Diamond-Blackfan anemia Pathogenic (Dec 16, 2019)link
19-41860789-T-A Diamond-Blackfan anemia Likely benign (Aug 10, 2020)link
19-41860789-TG-T Diamond-Blackfan anemia Pathogenic (Aug 28, 2021)link
19-41860791-TA-T Diamond-Blackfan anemia Pathogenic (Jun 09, 2017)link
19-41860794-AAG-CTCCAGCATCCAGTT not specified Uncertain significance (Aug 16, 2023)link
19-41860798-C-T Diamond-Blackfan anemia Likely benign (May 19, 2021)link
19-41860808-C-T Diamond-Blackfan anemia Pathogenic (Apr 05, 2018)link
19-41860817-G-T Pathogenic (Aug 03, 2015)link

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RPS19protein_codingprotein_codingENST00000598742 513007
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9210.078500000.00
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.455392.20.5750.00000596926
Missense in Polyphen214.2120.14073185
Synonymous-2.135437.41.440.00000238297
Loss of Function2.6408.140.003.90e-788

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000.00
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

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

loftool
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

AllRecessiveDominant
MendelianLowLowLow
Primary ImmunodeficiencyLowLowLow
CancerLowLowLow

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