NUDT17

nudix hydrolase 17, the group of Nudix hydrolase family

Basic information

Region (hg38): 1:145845630-145848954

Links

ENSG00000186364 ∙ NCBI:200035 ∙ ∙ HGNC:26618 ∙ Uniprot:P0C025 ∙ 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 NUDT17 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NUDT17 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			31	3		34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	3	0

Variants in NUDT17

This is a list of pathogenic ClinVar variants found in the NUDT17 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-145845644-G-A		not specified	Uncertain significance (Nov 03, 2023)
1-145845645-C-G		not specified	Uncertain significance (Jul 20, 2021)
1-145845647-G-A		not specified	Uncertain significance (Jul 27, 2024)
1-145845663-T-C		not specified	Uncertain significance (Mar 07, 2025)
1-145845663-T-G		not specified	Uncertain significance (Oct 02, 2023)
1-145845704-A-T		not specified	Uncertain significance (Nov 15, 2021)
1-145845705-G-C		not specified	Uncertain significance (Apr 30, 2024)
1-145845740-G-C		not specified	Uncertain significance (Mar 20, 2023)
1-145845743-A-C		not specified	Likely benign (Mar 07, 2023)
1-145845782-G-C		not specified	Uncertain significance (Oct 17, 2024)
1-145845821-C-G		not specified	Uncertain significance (Sep 10, 2024)
1-145846017-C-A		not specified	Uncertain significance (Dec 09, 2023)
1-145846062-C-T		not specified	Uncertain significance (Jun 23, 2023)
1-145846092-T-C		not specified	Uncertain significance (Sep 28, 2022)
1-145846146-C-T		not specified	Uncertain significance (Dec 11, 2024)
1-145846158-G-C		not specified	Uncertain significance (Dec 28, 2023)
1-145846160-A-T		not specified	Uncertain significance (Dec 10, 2024)
1-145846170-T-G		not specified	Uncertain significance (Jul 25, 2023)
1-145846638-G-A		not specified	Uncertain significance (Oct 07, 2024)
1-145846685-T-C		not specified	Uncertain significance (Aug 28, 2024)
1-145847287-A-G		not specified	Uncertain significance (Oct 04, 2024)
1-145847613-A-T		not specified	Uncertain significance (Jan 18, 2025)
1-145847617-C-T		not specified	Uncertain significance (Aug 01, 2023)
1-145847620-T-C		not specified	Uncertain significance (Dec 08, 2024)
1-145847673-A-G		not specified	Uncertain significance (Dec 11, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NUDT17	protein_coding	protein_coding	ENST00000334513	8	3325

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.11e-7	0.564	125665	0	83	125748	0.000330

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.730	205	178	1.15	0.00000867	2020
Missense in Polyphen		63	56.87	1.1078		702
Synonymous	-1.19	87	74.0	1.18	0.00000373	709
Loss of Function	1.01	13	17.6	0.739	9.11e-7	166

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000754	0.000688
Ashkenazi Jewish	0.00	0.00
East Asian	0.000443	0.000435
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000331	0.000308
Middle Eastern	0.000443	0.000435
South Asian	0.000589	0.000588
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probably mediates the hydrolysis of some nucleoside diphosphate derivatives. {ECO:0000250}.

Intolerance Scores

• loftool: 0.455
• rvis_EVS: -0.23
• rvis_percentile_EVS: 37.32

Haploinsufficiency Scores

• pHI: 0.280
• hipred: N
• hipred_score: 0.145
• ghis: 0.499

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 6.91e-7

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nudt17

Gene ontology

• Biological process: NADH metabolic process;NADP catabolic process;NAD catabolic process
• Cellular component: peroxisome;cytosol
• Molecular function: hydrolase activity;NADH pyrophosphatase activity;metal ion binding