RPS10-NUDT3

RPS10-NUDT3 readthrough

Basic information

Region (hg38): 6:34284887-34426071

Links

ENSG00000270800 ∙ NCBI:100529239 ∙ ∙ HGNC:49181 ∙ ∙ ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RPS10-NUDT3 gene.

• Congenital hypoplastic anemia (79 variants)
• Diamond-Blackfan anemia 9 (30 variants)
• not provided (24 variants)
• not specified (8 variants)
• Inborn genetic diseases (6 variants)
• RPS10-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPS10-NUDT3 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			3	25		28
missense			18	2	1	21
nonsense	3					3
start loss						0
frameshift	3	1				4
inframe indel			1			1
splice donor/acceptor (+/-2bp)		2	4	1	1	8
splice region						0
non coding			9	29	12	50
Total	6	3	35	57	14

Variants in RPS10-NUDT3

This is a list of pathogenic ClinVar variants found in the RPS10-NUDT3 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-34288761-T-A		not specified	Uncertain significance (Apr 06, 2022)
6-34288764-C-A		not specified	Uncertain significance (Jul 16, 2024)
6-34288899-C-T		not specified	Uncertain significance (Jun 25, 2024)
6-34392298-G-C		not specified	Uncertain significance (Oct 27, 2022)
6-34392346-G-A		not specified	Uncertain significance (Jan 29, 2024)
6-34417358-C-T			Likely benign (Apr 16, 2019)
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 • Diamond-Blackfan anemia 9	Uncertain significance (Apr 25, 2024)
6-34417516-G-T		Diamond-Blackfan anemia 9	Uncertain significance (Feb 01, 2024)
6-34417519-T-C		Diamond-Blackfan anemia 9	Uncertain significance (Jan 16, 2024)
6-34417523-C-A		Diamond-Blackfan anemia • Diamond-Blackfan anemia 9	Uncertain significance (May 29, 2024)
6-34417525-C-T		Diamond-Blackfan anemia	Uncertain significance (Nov 17, 2022)
6-34417531-C-T		Diamond-Blackfan anemia • Diamond-Blackfan anemia 9	Uncertain significance (Jun 01, 2024)
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	Conflicting classifications of pathogenicity (Apr 29, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RPS10-NUDT3	protein_coding	protein_coding	ENST00000605528	8	137279

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.952	0.0481	125741	0	7	125748	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.75	105	169	0.621	0.0000104	1849
Missense in Polyphen		10	21.666	0.46155		288
Synonymous	0.290	61	63.9	0.954	0.00000394	554
Loss of Function	3.54	2	18.3	0.109	0.00000105	202

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000938	0.0000913
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000880	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Ribosome - Homo sapiens (human) (Consensus)

Gene Damage Prediction

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

Gene ontology

• Biological process: ribosomal small subunit assembly
• Cellular component: cytosolic small ribosomal subunit
• Molecular function: structural constituent of ribosome;hydrolase activity