RPS10

ribosomal protein S10, the group of S ribosomal proteins

Basic information

Region (hg38): 6:34417454-34426069

Links

ENSG00000124614 ∙ NCBI:6204 ∙ OMIM:603632 ∙ HGNC:10383 ∙ Uniprot:P46783 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Diamond-Blackfan anemia 9 (Strong), mode of inheritance: AD
• Diamond-Blackfan anemia 9 (Strong), mode of inheritance: AD
• Diamond-Blackfan anemia 9 (Strong), mode of inheritance: AD
• Diamond-Blackfan anemia (Supportive), mode of inheritance: AD
• Diamond-Blackfan anemia (Definitive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Diamond-Blackfan anemia 9	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; Oncologic	16317735; 20116044; 20301769; 23812780

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RPS10 gene.

• Diamond-Blackfan anemia (4 variants)
• Diamond-Blackfan anemia 9 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPS10 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			2	31		33
missense			34	1	1	36
nonsense	1					1
start loss	1					1
frameshift	2	1				3
inframe indel			3			3
splice donor/acceptor (+/-2bp)		2				2
splice region			4	4	1	9
non coding			7	33	15	55
Total	4	3	46	65	16

Variants in RPS10

This is a list of pathogenic ClinVar variants found in the RPS10 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-34417463-T-C		Diamond-Blackfan anemia 9	Benign (Jan 12, 2018)
6-34417481-C-A		Diamond-Blackfan anemia 9	Uncertain significance (Jan 12, 2018)
6-34417511-G-C		Diamond-Blackfan anemia	Uncertain significance (Dec 11, 2021)
6-34417523-C-A		Diamond-Blackfan anemia	Uncertain significance (Oct 25, 2023)
6-34417525-C-T		Diamond-Blackfan anemia	Uncertain significance (Nov 17, 2022)
6-34417531-C-T		Diamond-Blackfan anemia	Uncertain significance (Mar 18, 2022)
6-34417533-A-T		Diamond-Blackfan anemia	Likely benign (Jul 21, 2023)
6-34417541-C-T		Diamond-Blackfan anemia	Uncertain significance (Mar 04, 2022)
6-34417542-G-A		Diamond-Blackfan anemia	Likely benign (Sep 05, 2023)
6-34417547-T-C		Diamond-Blackfan anemia	Uncertain significance (Sep 25, 2023)
6-34417553-A-G		Diamond-Blackfan anemia	Likely benign (Dec 06, 2023)
6-34417721-A-G			Likely benign (Mar 20, 2019)
6-34417740-A-T			Benign (Jul 17, 2018)
6-34418142-G-GT			Benign (Dec 21, 2018)
6-34418362-TACTC-T		Diamond-Blackfan anemia	Uncertain significance (Jul 31, 2020)
6-34418381-G-A		not specified • Diamond-Blackfan anemia 9 • Diamond-Blackfan anemia	Benign/Likely benign (Jan 22, 2024)
6-34418388-G-A		Diamond-Blackfan anemia 9	Benign (Jan 13, 2018)
6-34418393-A-C		Diamond-Blackfan anemia 9 • Diamond-Blackfan anemia	Benign/Likely benign (Nov 27, 2023)
6-34418400-G-A		Diamond-Blackfan anemia	Uncertain significance (Mar 29, 2021)
6-34418405-G-A		Diamond-Blackfan anemia	Likely benign (Dec 08, 2023)
6-34418416-C-T		Diamond-Blackfan anemia • not specified	Uncertain significance (Jan 19, 2024)
6-34418417-G-A		Diamond-Blackfan anemia • not specified • Diamond-Blackfan anemia 9 • RPS10-NUDT3-related disorder • RPS10-related disorder	Benign/Likely benign (Jan 31, 2024)
6-34418417-G-T		Diamond-Blackfan anemia	Likely benign (Dec 11, 2023)
6-34418422-C-A		Diamond-Blackfan anemia • not specified	Uncertain significance (Dec 13, 2023)
6-34418426-T-C		Diamond-Blackfan anemia	Likely pathogenic (May 20, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RPS10	protein_coding	protein_coding	ENST00000326199	5	8672

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.971	0.0289	125746	0	2	125748	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.24	67	102	0.655	0.00000697	1061
Missense in Polyphen		5	14.13	0.35386		225
Synonymous	0.764	30	35.8	0.838	0.00000216	326
Loss of Function	3.07	0	10.9	0.00	7.38e-7	106

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000640	0.0000615
Ashkenazi Jewish	0.0000992	0.0000992
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

• Function: FUNCTION: Component of the 40S ribosomal subunit.
• Disease: DISEASE: Diamond-Blackfan anemia 9 (DBA9) [MIM:613308]: 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:20116044}. 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;EGFR1;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: 0.105

Intolerance Scores

• rvis_EVS: -0.14
• rvis_percentile_EVS: 42.88

Haploinsufficiency Scores

• pHI: 0.247
• hipred: Y
• hipred_score: 0.681
• ghis: 0.572

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.961

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Rps10

Gene ontology

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