NUDT13

nudix hydrolase 13, the group of Nudix hydrolase family

Basic information

Region (hg38): 10:73110374-73131828

Links

ENSG00000166321 ∙ NCBI:25961 ∙ OMIM:609233 ∙ HGNC:18827 ∙ Uniprot:Q86X67 ∙ 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 NUDT13 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NUDT13 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			27	1		28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	1	0

Variants in NUDT13

This is a list of pathogenic ClinVar variants found in the NUDT13 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-73114447-C-T		not specified	Uncertain significance (Dec 26, 2023)
10-73120040-G-T		not specified	Uncertain significance (Feb 17, 2024)
10-73120137-C-G		not specified	Uncertain significance (Jun 23, 2023)
10-73120143-G-A		not specified	Likely benign (Jan 07, 2022)
10-73122189-C-G		not specified	Uncertain significance (Aug 16, 2021)
10-73122219-A-G		not specified	Uncertain significance (Oct 25, 2022)
10-73122303-A-C		not specified	Uncertain significance (Feb 11, 2022)
10-73124319-C-T		not specified	Uncertain significance (Nov 07, 2022)
10-73125133-C-T		not specified	Uncertain significance (Aug 10, 2021)
10-73125136-T-G		not specified	Uncertain significance (Nov 10, 2022)
10-73125154-T-C		not specified	Uncertain significance (Oct 03, 2022)
10-73125178-A-C		not specified	Uncertain significance (Nov 10, 2022)
10-73125179-C-T		not specified	Uncertain significance (Apr 06, 2022)
10-73125197-G-A		not specified	Uncertain significance (Nov 17, 2023)
10-73125200-G-A		not specified	Uncertain significance (Jan 27, 2022)
10-73125226-A-G		not specified	Uncertain significance (Feb 15, 2023)
10-73125438-G-A		not specified	Uncertain significance (Jun 13, 2022)
10-73125447-T-C		not specified	Uncertain significance (Nov 09, 2021)
10-73125477-T-G		not specified	Uncertain significance (May 27, 2022)
10-73125507-T-C		not specified	Uncertain significance (Jan 10, 2022)
10-73126691-C-G		not specified	Uncertain significance (Nov 15, 2021)
10-73126696-C-T		not specified	Uncertain significance (Dec 19, 2022)
10-73126706-T-C		not specified	Uncertain significance (Dec 03, 2021)
10-73126817-G-A		not specified	Uncertain significance (May 24, 2024)
10-73130719-G-C		not specified	Uncertain significance (May 03, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NUDT13	protein_coding	protein_coding	ENST00000357321	8	21370

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.62e-12	0.0662	122061	234	3451	125746	0.0148

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.512	168	188	0.895	0.00000944	2274
Missense in Polyphen		50	70.365	0.71058		844
Synonymous	1.01	60	70.8	0.847	0.00000330	684
Loss of Function	0.284	18	19.4	0.930	9.93e-7	219

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.175	0.175
Ashkenazi Jewish	0.0157	0.0155
East Asian	0.00114	0.00114
Finnish	0.00213	0.00213
European (Non-Finnish)	0.00497	0.00496
Middle Eastern	0.00114	0.00114
South Asian	0.00248	0.00245
Other	0.00832	0.00834

dbNSFP

Source: dbNSFP

• Pathway: Metabolism of nucleotides;Interconversion of nucleotide di- and triphosphates;Metabolism (Consensus)

Recessive Scores

• pRec: 0.101

Intolerance Scores

• loftool: 0.879
• rvis_EVS: 0.91
• rvis_percentile_EVS: 89.47

Haploinsufficiency Scores

• pHI: 0.161
• hipred: N
• hipred_score: 0.292
• ghis: 0.427

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.410

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nudt13

Gene ontology

• Biological process: nucleobase-containing small molecule interconversion
• Cellular component: mitochondrial matrix
• Molecular function: pyrophosphatase activity;metal ion binding