RPS28

ribosomal protein S28, the group of S ribosomal proteins

Basic information

Region (hg38): 19:8321158-8323340

Links

ENSG00000233927 ∙ NCBI:6234 ∙ OMIM:603685 ∙ HGNC:10418 ∙ Uniprot:P62857 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Diamond-Blackfan anemia 15 with mandibulofacial dysostosis	AD	Audiologic/Otolaryngologic; Hematologic; Oncologic	Early 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 management	Audiologic/Otolaryngologic; Craniofacial; Hematologic; Musculoskeletal; Oncologic	11424144; 24942156

ClinVar

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

• Diamond-Blackfan anemia 15 with mandibulofacial dysostosis (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				9		9
missense			2			2
nonsense						0
start loss	1					1
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				3		3
non coding			1	2	5	8
Total	1	0	3	11	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)
19-8321175-T-G			Benign (Jun 20, 2021)
19-8321337-T-C		not specified	Uncertain significance (Feb 21, 2024)
19-8321354-G-A		not specified	Uncertain significance (Dec 13, 2022)
19-8321422-G-A			Benign (May 14, 2021)
19-8321483-C-T			Benign (Aug 27, 2019)
19-8321531-A-G		Diamond-Blackfan anemia 15 with mandibulofacial dysostosis	Pathogenic (Jun 08, 2022)
19-8321536-C-T			Likely benign (Mar 20, 2023)
19-8321537-A-G			Uncertain significance (Sep 05, 2023)
19-8321542-C-T			Likely benign (Aug 22, 2022)
19-8321545-T-C			Likely benign (Dec 13, 2023)
19-8321563-G-A			Likely benign (Sep 12, 2023)
19-8321589-T-C			Likely benign (Aug 27, 2023)
19-8321589-T-G			Benign (Jan 02, 2024)
19-8321642-C-T			Likely benign (May 22, 2023)
19-8321649-C-T			Likely benign (Sep 26, 2022)
19-8321667-C-T			Likely benign (Feb 09, 2023)
19-8321709-C-T			Likely benign (May 25, 2018)
19-8321710-G-T			Likely benign (Oct 25, 2022)
19-8321778-T-C			Benign (May 16, 2021)
19-8321817-G-A			Benign (May 14, 2021)
19-8321979-G-T		RPS28-related disorder	Likely benign (Dec 30, 2022)
19-8322012-C-G			Likely benign (Jul 26, 2023)
19-8322022-G-A			Uncertain significance (May 24, 2023)
19-8322067-T-C			Likely benign (Sep 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RPS28	protein_coding	protein_coding	ENST00000600659	3	2183

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.683	0.300	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.51	12	38.4	0.313	0.00000176	425
Missense in Polyphen		0	6.442	0		108
Synonymous	-0.912	20	15.4	1.30	6.88e-7	140
Loss of Function	1.79	0	3.75	0.00	1.63e-7	43

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

• 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

• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.04

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.528
• ghis: 0.428

Essentials

• essential_gene_CRISPR: E
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.833

Gene Damage Prediction

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

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