NUDT9

nudix hydrolase 9, the group of Nudix hydrolase family

Basic information

Region (hg38): 4:87422573-87459455

Links

ENSG00000170502 ∙ NCBI:53343 ∙ OMIM:606022 ∙ HGNC:8056 ∙ Uniprot:Q9BW91 ∙ 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 NUDT9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NUDT9 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			28			28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	28	0	0

Variants in NUDT9

This is a list of pathogenic ClinVar variants found in the NUDT9 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-87422934-T-C		not specified	Uncertain significance (Sep 26, 2024)
4-87422946-C-G		not specified	Uncertain significance (Mar 07, 2024)
4-87423003-A-G		not specified	Uncertain significance (Sep 11, 2024)
4-87434994-T-A		not specified	Uncertain significance (Dec 07, 2022)
4-87435009-C-T		not specified	Uncertain significance (Jan 04, 2024)
4-87435018-A-G		not specified	Uncertain significance (Aug 21, 2024)
4-87435019-A-G		not specified	Uncertain significance (Feb 06, 2024)
4-87435043-C-A		not specified	Uncertain significance (Oct 26, 2022)
4-87435066-G-T		not specified	Uncertain significance (Jan 03, 2025)
4-87435069-C-T		not specified	Uncertain significance (Feb 13, 2024)
4-87435078-C-A		not specified	Uncertain significance (Mar 29, 2022)
4-87435114-C-T		not specified	Uncertain significance (Aug 14, 2024)
4-87435124-A-G		not specified	Uncertain significance (Mar 08, 2024)
4-87435195-C-A		not specified	Uncertain significance (Dec 10, 2024)
4-87438277-T-C		not specified	Likely benign (Aug 08, 2023)
4-87438305-G-A		not specified	Uncertain significance (Aug 05, 2024)
4-87441860-C-T		not specified	Uncertain significance (Sep 30, 2024)
4-87441908-A-G		not specified	Uncertain significance (Apr 01, 2024)
4-87449192-A-G		not specified	Uncertain significance (Oct 25, 2022)
4-87449212-G-T		not specified	Uncertain significance (Feb 06, 2024)
4-87451595-G-A		not specified	Uncertain significance (Jun 17, 2024)
4-87451617-G-A		not specified	Uncertain significance (Oct 29, 2024)
4-87451698-A-G		not specified	Uncertain significance (Aug 14, 2023)
4-87454374-T-C		not specified	Uncertain significance (Dec 03, 2024)
4-87454405-C-A		not specified	Uncertain significance (Sep 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NUDT9	protein_coding	protein_coding	ENST00000302174	8	36873

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000918	0.935	125691	0	54	125745	0.000215

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.03	151	191	0.790	0.00000958	2298
Missense in Polyphen		41	68.127	0.60182		778
Synonymous	-0.452	73	68.2	1.07	0.00000363	648
Loss of Function	1.74	11	19.2	0.572	0.00000106	211

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000454	0.000452
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000345	0.000343
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.000330	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Hydrolyzes ADP-ribose (ADPR) to AMP and ribose 5'- phosphate.
• Pathway: Purine metabolism - Homo sapiens (human);Nucleobase catabolism;Metabolism of nucleotides;Metabolism;Purine nucleotides nucleosides metabolism;Phosphate bond hydrolysis by NUDT proteins;Purine catabolism (Consensus)

Recessive Scores

• pRec: 0.128

Intolerance Scores

• loftool: 0.883
• rvis_EVS: 0.08
• rvis_percentile_EVS: 60.31

Haploinsufficiency Scores

• pHI: 0.0672
• hipred: N
• hipred_score: 0.265
• ghis: 0.520

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0403

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nudt9

Gene ontology

• Biological process: nucleobase-containing small molecule catabolic process;ADP catabolic process;IDP catabolic process
• Cellular component: mitochondrial matrix;extracellular exosome
• Molecular function: ADP-sugar diphosphatase activity;adenosine-diphosphatase activity;ADP-ribose diphosphatase activity