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GeneBe

RPS28

ribosomal protein S28, the group of S ribosomal proteins

Basic information

Region (hg38): 19:8321157-8323340

Links

ENSG00000233927NCBI:6234OMIM:603685HGNC:10418Uniprot:P62857AlphaFoldGenCCjaxSfariGnomADPubmed

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 (14 variants)
  • Diamond-Blackfan anemia 15 with mandibulofacial dysostosis (2 variants)
  • Inborn genetic diseases (2 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.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous 3 3
missense 0
nonsense 1 1
start loss 0
frameshift 0
inframe indel 0
splice variant 2 2
non coding 2 9 11
Total 1 0 2 5 9

Variants in RPS28

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

Position Type Phenotype Significance ClinVar
19-8321172-G-C Benign (Jun 20, 2021)link
19-8321175-T-G Benign (Jun 20, 2021)link
19-8321354-G-A Inborn genetic diseases Uncertain significance (Dec 13, 2022)link
19-8321422-G-A Benign (May 14, 2021)link
19-8321483-C-T Benign (Aug 27, 2019)link
19-8321531-A-G Diamond-Blackfan anemia 15 with mandibulofacial dysostosis Pathogenic (Jun 08, 2022)link
19-8321536-C-T Likely benign (Sep 05, 2022)link
19-8321542-C-T Likely benign (Aug 22, 2022)link
19-8321589-T-G Benign (Oct 04, 2022)link
19-8321649-C-T Likely benign (Sep 26, 2022)link
19-8321709-C-T Likely benign (May 25, 2018)link
19-8321778-T-C Benign (May 16, 2021)link
19-8321817-G-A Benign (May 14, 2021)link
19-8322067-T-C Likely benign (Sep 01, 2022)link
19-8322069-G-A Likely benign (Sep 13, 2022)link
19-8322114-T-C Diamond-Blackfan anemia 15 with mandibulofacial dysostosis Benign (Nov 07, 2021)link
19-8322323-G-A Benign (Nov 12, 2018)link
19-8322919-C-T Inborn genetic diseases Uncertain significance (Jan 05, 2022)link

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