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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:P39019AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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

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 (144 variants)
  • Diamond-Blackfan anemia 1 (44 variants)
  • not provided (38 variants)
  • not specified (13 variants)
  • RPS19-related condition (2 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.

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
clinvar
32
clinvar
36
missense
6
clinvar
10
clinvar
32
clinvar
48
nonsense
10
clinvar
1
clinvar
1
clinvar
12
start loss
3
clinvar
1
clinvar
4
frameshift
20
clinvar
1
clinvar
1
clinvar
22
inframe indel
1
clinvar
1
clinvar
2
splice donor/acceptor (+/-2bp)
4
clinvar
5
clinvar
9
splice region
9
2
1
12
non coding
9
clinvar
24
clinvar
8
clinvar
41
Total 43 18 49 56 8

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)2683504
19-41860264-C-T Diamond-Blackfan anemia 1 Uncertain significance (Jan 13, 2018)893194
19-41860280-A-G Diamond-Blackfan anemia 1 Likely benign (Jan 13, 2018)329387
19-41860303-C-T Diamond-Blackfan anemia 1 Uncertain significance (Jan 12, 2018)329388
19-41860315-G-T Diamond-Blackfan anemia Benign (May 01, 2023)1164625
19-41860325-C-C not specified Benign (Aug 08, 2016)440244
19-41860383-C-G Benign (Mar 03, 2015)1239177
19-41860761-A-G Diamond-Blackfan anemia 1 Likely benign (Aug 22, 2021)329389
19-41860762-C-T Diamond-Blackfan anemia 1 Benign/Likely benign (Sep 14, 2021)894042
19-41860766-C-A Diamond-Blackfan anemia 1 Likely benign (Jan 12, 2018)329390
19-41860766-C-T Diamond-Blackfan anemia 1 • not specified Uncertain significance (Mar 02, 2021)2435479
19-41860768-C-T not specified • Diamond-Blackfan anemia 1 Conflicting classifications of pathogenicity (Jan 12, 2018)436552
19-41860775-A-C Diamond-Blackfan anemia Pathogenic (Oct 22, 2023)2780439
19-41860775-A-G Diamond-Blackfan anemia 1 Uncertain significance (May 22, 2022)1687343
19-41860777-G-A Diamond-Blackfan anemia Pathogenic (Jul 29, 2022)860401
19-41860777-G-C Diamond-Blackfan anemia Pathogenic (Aug 04, 2016)1736908
19-41860777-G-T Diamond-Blackfan anemia • Diamond-Blackfan anemia 1 Pathogenic (Feb 04, 2023)372494
19-41860780-T-G Diamond-Blackfan anemia Likely benign (Apr 22, 2023)1563472
19-41860784-G-T Diamond-Blackfan anemia Uncertain significance (Aug 28, 2021)953930
19-41860786-T-TA Diamond-Blackfan anemia Pathogenic (Dec 16, 2019)858368
19-41860789-T-A Diamond-Blackfan anemia Likely benign (Aug 10, 2020)1133136
19-41860789-TG-T Diamond-Blackfan anemia Pathogenic (Oct 11, 2019)940580
19-41860791-TA-T Diamond-Blackfan anemia Pathogenic (Jun 09, 2017)1787597
19-41860794-AAG-CTCCAGCATCCAGTT not specified Uncertain significance (Aug 16, 2023)2581165
19-41860798-C-T Diamond-Blackfan anemia Likely benign (Oct 25, 2023)1619870

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