NUDT6

nudix hydrolase 6, the group of Nudix hydrolase family

Basic information

Region (hg38): 4:122888696-122922968

Links

ENSG00000170917 ∙ NCBI:11162 ∙ OMIM:606261 ∙ HGNC:8053 ∙ Uniprot:P53370 ∙ 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 NUDT6 gene.

• Inborn genetic diseases (11 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NUDT6 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			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	11	0	1

Variants in NUDT6

This is a list of pathogenic ClinVar variants found in the NUDT6 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-122892221-C-T		not specified	Uncertain significance (Oct 05, 2023)
4-122892265-A-G		not specified	Uncertain significance (May 10, 2022)
4-122892274-C-T		not specified	Uncertain significance (Nov 10, 2022)
4-122892388-A-C		not specified	Uncertain significance (Jan 17, 2024)
4-122893009-G-A		NUDT6-related disorder	Benign (Jan 17, 2020)
4-122893015-G-A		NUDT6-related disorder	Likely benign (Aug 21, 2022)
4-122893077-G-T		not specified	Uncertain significance (Jan 08, 2024)
4-122893166-C-A		not specified	Uncertain significance (Jan 23, 2023)
4-122893167-G-A		NUDT6-related disorder	Likely benign (Sep 09, 2019)
4-122893210-C-T		not specified	Uncertain significance (Dec 15, 2022)
4-122893230-G-T		NUDT6-related disorder	Benign (Aug 10, 2019)
4-122912575-C-T		not specified	Uncertain significance (Nov 01, 2021)
4-122917620-G-C		not specified	Uncertain significance (Jun 29, 2023)
4-122917623-G-C		not specified	Uncertain significance (Jun 07, 2023)
4-122917690-A-T		not specified	Uncertain significance (Oct 04, 2022)
4-122922412-C-T		not specified	Uncertain significance (Jul 20, 2021)
4-122922430-C-T		not specified	Uncertain significance (Jan 20, 2023)
4-122922500-C-G		not specified	Uncertain significance (Apr 14, 2022)
4-122922502-G-T		not specified	Uncertain significance (Jan 23, 2024)
4-122922518-C-G		NUDT6-related disorder	Benign (Jan 06, 2020)
4-122922530-C-T		not specified	Uncertain significance (Aug 09, 2021)
4-122922551-C-T		not specified	Uncertain significance (Feb 07, 2023)
4-122922773-G-A			Benign (Jul 21, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NUDT6	protein_coding	protein_coding	ENST00000304430	5	34272

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000291	0.939	125569	0	179	125748	0.000712

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0242	175	174	1.01	0.00000852	1991
Missense in Polyphen		70	74.543	0.93905		932
Synonymous	-0.765	82	73.6	1.11	0.00000380	652
Loss of Function	1.73	10	17.9	0.559	0.00000107	171

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000454	0.000450
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000370	0.000370
European (Non-Finnish)	0.00133	0.00130
Middle Eastern	0.00	0.00
South Asian	0.000231	0.000229
Other	0.000819	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May contribute to the regulation of cell proliferation. {ECO:0000269|PubMed:11266510}.

Recessive Scores

• pRec: 0.256

Intolerance Scores

• loftool: 0.784
• rvis_EVS: 0.64
• rvis_percentile_EVS: 83.9

Haploinsufficiency Scores

• pHI: 0.297
• hipred: N
• hipred_score: 0.253
• ghis: 0.464

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.194

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nudt6

Gene ontology

• Biological process: negative regulation of cell population proliferation;negative regulation of cell cycle
• Cellular component: nucleus;cytoplasm;mitochondrion
• Molecular function: NADH pyrophosphatase activity;ADP-ribose diphosphatase activity;NAD binding