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RPS28

ribosomal protein S28, the group of S ribosomal proteins

Basic information

Region (hg38): 19:8321157-8323340

Links

ENSG00000233927NCBI:6234OMIM:603685HGNC:10418Uniprot:P62857AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • Diamond-Blackfan anemia 15 with mandibulofacial dysostosis (Moderate), mode of inheritance: AD
  • Diamond-Blackfan anemia (Supportive), mode of inheritance: AD
  • Diamond-Blackfan anemia 15 with mandibulofacial dysostosis (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Diamond-Blackfan anemia 15 with mandibulofacial dysostosisADAudiologic/Otolaryngologic; Hematologic; OncologicEarly recognition and treatment of hearing impairment may improve outcomes, including speech and language development; Specific treatment of anemia (eg, steroids, regular transfusions) can be effective; surveillance for and early treatment of malignancy may be beneficial; Individuals with DBA may manifest a variety of congenital malformations, and awareness may allow prompt detection and managementAudiologic/Otolaryngologic; Craniofacial; Hematologic; Musculoskeletal; Oncologic11424144; 24942156

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RPS28 gene.

  • not provided (13 variants)
  • Diamond-Blackfan anemia 15 with mandibulofacial dysostosis (2 variants)
  • Inborn genetic diseases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPS28 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
6
clinvar
6
missense
0
nonsense
0
start loss
1
clinvar
1
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
2
2
non coding
1
clinvar
5
clinvar
6
Total 1 0 1 6 5

Variants in RPS28

This is a list of pathogenic ClinVar variants found in the RPS28 region.

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

Position Type Phenotype Significance ClinVar
19-8321172-G-C Benign (Jun 20, 2021)1224045
19-8321175-T-G Benign (Jun 20, 2021)1265048
19-8321337-T-C not specified Uncertain significance (Feb 21, 2024)3187151
19-8321354-G-A not specified Uncertain significance (Dec 13, 2022)2334462
19-8321422-G-A Benign (May 14, 2021)1276445
19-8321483-C-T Benign (Aug 27, 2019)1257584
19-8321531-A-G Diamond-Blackfan anemia 15 with mandibulofacial dysostosis Pathogenic (Jun 08, 2022)187848
19-8321536-C-T Likely benign (Mar 20, 2023)2056150
19-8321537-A-G Uncertain significance (Sep 05, 2023)2916205
19-8321542-C-T Likely benign (Aug 22, 2022)2026349
19-8321545-T-C Likely benign (Dec 13, 2023)2702974
19-8321563-G-A Likely benign (Sep 12, 2023)2760399
19-8321589-T-C Likely benign (Aug 27, 2023)2798271
19-8321589-T-G Benign (Jan 02, 2024)1971128
19-8321642-C-T Likely benign (May 22, 2023)2867901
19-8321649-C-T Likely benign (Sep 26, 2022)2155844
19-8321667-C-T Likely benign (Feb 09, 2023)2835784
19-8321709-C-T Likely benign (May 25, 2018)668538
19-8321710-G-T Likely benign (Oct 25, 2022)2896698
19-8321778-T-C Benign (May 16, 2021)1268375
19-8321817-G-A Benign (May 14, 2021)1181154
19-8321979-G-T RPS28-related condition Likely benign (Dec 30, 2022)2793487
19-8322012-C-G Likely benign (Jul 26, 2023)2897022
19-8322022-G-A Uncertain significance (May 24, 2023)2881770
19-8322067-T-C Likely benign (Sep 01, 2022)2649195

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RPS28protein_codingprotein_codingENST00000600659 32183
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.6830.30000000.00
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.511238.40.3130.00000176425
Missense in Polyphen06.4420108
Synonymous-0.9122015.41.306.88e-7140
Loss of Function1.7903.750.001.63e-743

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

Disease
DISEASE: Diamond-Blackfan anemia 15, with mandibulofacial dysostosis (DBA15) [MIM:606164]: A form of Diamond-Blackfan anemia, a congenital non-regenerative hypoplastic anemia that usually presents early in infancy. Diamond-Blackfan anemia is characterized by a moderate to severe macrocytic anemia, erythroblastopenia, and an increased risk of malignancy. 30 to 40% of Diamond-Blackfan anemia patients present with short stature and congenital anomalies, the most frequent being craniofacial (Pierre-Robin syndrome and cleft palate), thumb and urogenital anomalies. {ECO:0000269|PubMed:24942156}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
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)

Intolerance Scores

loftool
rvis_EVS
0.17
rvis_percentile_EVS
65.04

Haploinsufficiency Scores

pHI
hipred
Y
hipred_score
0.528
ghis
0.428

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
essential_gene_gene_trap
H
gene_indispensability_pred
E
gene_indispensability_score
0.833

Gene Damage Prediction

AllRecessiveDominant
MendelianLowLowLow
Primary ImmunodeficiencyLowLowLow
CancerLowLowLow

Mouse Genome Informatics

Gene name
Rps28
Phenotype
normal phenotype;

Zebrafish Information Network

Gene name
rps28
Affected structure
whole organism
Phenotype tag
abnormal
Phenotype quality
decreased size

Gene ontology

Biological process
ribosomal small subunit assembly;nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;cytoplasmic translation;rRNA processing;translation;translational initiation;SRP-dependent cotranslational protein targeting to membrane;maturation of SSU-rRNA;ribosome biogenesis;ribosomal small subunit biogenesis
Cellular component
nucleoplasm;cytosol;small ribosomal subunit;cytosolic small ribosomal subunit;polysomal ribosome;extracellular exosome;cytoplasmic side of rough endoplasmic reticulum membrane
Molecular function
RNA binding;structural constituent of ribosome;protein binding