NUDT10

nudix hydrolase 10, the group of Nudix hydrolase family

Basic information

Region (hg38): X:51332231-51337525

Links

ENSG00000122824 ∙ NCBI:170685 ∙ OMIM:300527 ∙ HGNC:17621 ∙ Uniprot:Q8NFP7 ∙ AlphaFold ∙ 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 NUDT10 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NUDT10 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						0
missense			5	2		7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	2	0

Variants in NUDT10

This is a list of pathogenic ClinVar variants found in the NUDT10 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-51332990-C-G		not specified	Uncertain significance (Apr 25, 2022)
X-51333051-G-A		not specified	Uncertain significance (Dec 12, 2023)
X-51333119-A-C		not specified	Uncertain significance (May 28, 2024)
X-51333119-A-G		not specified	Uncertain significance (Sep 27, 2021)
X-51333209-G-A		not specified	Likely benign (Dec 05, 2024)
X-51333227-G-C			Likely benign (Dec 01, 2022)
X-51333239-A-G		not specified	Uncertain significance (Jul 13, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NUDT10	protein_coding	protein_coding	ENST00000376006	1	5295

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.106	0.785	125706	1	4	125711	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.979	43	65.3	0.659	0.00000427	1053
Missense in Polyphen		13	27.254	0.47699		413
Synonymous	-1.09	39	31.2	1.25	0.00000208	331
Loss of Function	1.25	2	5.03	0.398	3.19e-7	81

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000760	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000734	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000367	0.0000264
Middle Eastern	0.0000734	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cleaves a beta-phosphate from the diphosphate groups in PP-InsP5 (diphosphoinositol pentakisphosphate), suggesting that it may play a role in signal transduction. Also able to catalyze the hydrolysis of dinucleoside oligophosphates, with Ap6A and Ap5A being the preferred substrates. The major reaction products are ADP and p4a from Ap6A and ADP and ATP from Ap5A. Also able to hydrolyze 5-phosphoribose 1-diphosphate. {ECO:0000269|PubMed:12105228}.
• Pathway: Metabolism;Synthesis of pyrophosphates in the cytosol;Inositol phosphate metabolism (Consensus)

Recessive Scores

• pRec: 0.112

Intolerance Scores

• loftool: 0.221
• rvis_EVS: -0.08
• rvis_percentile_EVS: 47.79

Haploinsufficiency Scores

• pHI: 0.131
• ghis: 0.532

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nudt11

Gene ontology

• Biological process: inositol phosphate metabolic process;diphosphoinositol polyphosphate metabolic process;diadenosine pentaphosphate catabolic process;diadenosine hexaphosphate catabolic process;adenosine 5'-(hexahydrogen pentaphosphate) catabolic process
• Cellular component: nucleus;cytoplasm;cytosol
• Molecular function: endopolyphosphatase activity;protein binding;diphosphoinositol-polyphosphate diphosphatase activity;bis(5'-adenosyl)-hexaphosphatase activity;bis(5'-adenosyl)-pentaphosphatase activity;metal ion binding;m7G(5')pppN diphosphatase activity;inositol diphosphate tetrakisphosphate diphosphatase activity;inositol bisdiphosphate tetrakisphosphate diphosphatase activity;inositol diphosphate pentakisphosphate diphosphatase activity;inositol-1-diphosphate-2,3,4,5,6-pentakisphosphate diphosphatase activity;inositol-3-diphosphate-1,2,4,5,6-pentakisphosphate diphosphatase activity;inositol-5-diphosphate-1,2,3,4,6-pentakisphosphate diphosphatase activity;inositol-1,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 1-diphosphatase activity;inositol-1,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity;inositol-3,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity