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. These statistics are base on transcript: . Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			3 clinvar	25 clinvar		28
missense			18 clinvar	2 clinvar	1 clinvar	21
nonsense	3 clinvar					3
start loss						0
frameshift	3 clinvar	1 clinvar				4
splice donor/acceptor (+/-2bp)		2 clinvar	4 clinvar	1 clinvar	1 clinvar	8
Total	6	3	25	28	2

Loading clinvar variants...

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