RPS17

ribosomal protein S17, the group of S ribosomal proteins

Basic information

Region (hg38): 15:82536750-82540459

Previous symbols: [ "RPS17L" ]

Links

ENSG00000182774 ∙ NCBI:6218 ∙ OMIM:180472 ∙ HGNC:10397 ∙ Uniprot:P08708 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Diamond-Blackfan anemia 4 (Strong), mode of inheritance: AD
• Diamond-Blackfan anemia (Supportive), mode of inheritance: AD
• Diamond-Blackfan anemia 4 (Strong), mode of inheritance: AD
• Diamond-Blackfan anemia 4 (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Diamond-Blackfan anemia 4	AD	Hematologic; Oncologic	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	Craniofacial; Hematologic; Musculoskeletal; Oncologic	16317735; 17647292; 19061985; 20301769; 23718193; 23812780

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RPS17 gene.

• Diamond-Blackfan anemia (3 variants)
• not provided (1 variants)
• Diamond-Blackfan anemia 4 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPS17 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				5		5
missense			1			1
nonsense						0
start loss	2					2
frameshift	1					1
inframe indel			1			1
splice donor/acceptor (+/-2bp)		1				1
splice region				1		1
non coding					2	2
Total	3	1	2	5	2

Variants in RPS17

This is a list of pathogenic ClinVar variants found in the RPS17 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-82536819-C-T		Diamond-Blackfan anemia	Likely benign (Oct 09, 2018)
15-82536888-C-T		Diamond-Blackfan anemia 4	Likely benign (Aug 04, 2021)
15-82538226-C-T		not specified	Benign (May 04, 2022)
15-82538321-T-C		Diamond-Blackfan anemia 4 • Diamond-Blackfan anemia	Likely benign (Oct 18, 2021)
15-82538938-CCT-C		Diamond-Blackfan anemia 4	Pathogenic (Dec 01, 2008)
15-82538982-A-C		Diamond-Blackfan anemia 4	Pathogenic (Aug 01, 2013)
15-82538982-A-G		not specified • Diamond-Blackfan anemia	Conflicting classifications of pathogenicity (Feb 16, 2017)
15-82538986-C-T		Diamond-Blackfan anemia 4	Likely pathogenic (Dec 16, 2022)
15-82539981-CCTG-C			Uncertain significance (Dec 16, 2020)
15-82540006-T-G		RPS17-related condition	Uncertain significance (Jul 25, 2024)
15-82540010-G-A		Diamond-Blackfan anemia	Likely benign (Oct 19, 2021)
15-82540075-AG-A		Diamond-Blackfan anemia	Pathogenic (Dec 22, 2015)
15-82540091-G-A		Diamond-Blackfan anemia	Likely benign (Nov 18, 2015)
15-82540097-G-A		Diamond-Blackfan anemia	Likely benign (Oct 26, 2023)
15-82540122-C-A			Uncertain significance (Dec 21, 2022)
15-82540294-G-C			Benign (Sep 15, 2019)
15-82540427-A-C		Diamond-Blackfan anemia 4 • Diamond-Blackfan anemia	Pathogenic (Oct 14, 2015)
15-82540428-T-C		Diamond-Blackfan anemia	Pathogenic (Mar 25, 2015)
15-82540460-G-A		not specified	Benign (May 04, 2022)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP

• Disease: DISEASE: Diamond-Blackfan anemia 4 (DBA4) [MIM:612527]: 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 developing leukemia. 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:17647292, ECO:0000269|PubMed:19061985}. 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)

Recessive Scores

• pRec: 0.216

Haploinsufficiency Scores

• pHI: 0.853
• ghis: 0.409

Essentials

• essential_gene_CRISPR: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.801

Mouse Genome Informatics

• Gene name: Rps17

Gene ontology

• Biological process: nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;rRNA processing;translation;translational initiation;SRP-dependent cotranslational protein targeting to membrane;erythrocyte homeostasis;ribosomal small subunit biogenesis
• Cellular component: nucleoplasm;cytosol;ribosome;focal adhesion;membrane;cytosolic small ribosomal subunit
• Molecular function: RNA binding;structural constituent of ribosome