NUDT7

nudix hydrolase 7, the group of Nudix hydrolase family

Basic information

Region (hg38): 16:77722491-77742260

Links

ENSG00000140876 ∙ NCBI:283927 ∙ OMIM:609231 ∙ HGNC:8054 ∙ Uniprot:P0C024 ∙ 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 NUDT7 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 NUDT7 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			10	1		11
nonsense					1	1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	1	1

Variants in NUDT7

This is a list of pathogenic ClinVar variants found in the NUDT7 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-77722604-G-T			Benign (Aug 13, 2018)
16-77722605-A-T		not specified	Uncertain significance (Dec 16, 2023)
16-77725459-C-T		not specified	Uncertain significance (Dec 17, 2023)
16-77725495-C-T		not specified	Uncertain significance (Apr 04, 2023)
16-77735895-C-A		not specified	Uncertain significance (Dec 20, 2023)
16-77735928-T-C		not specified	Uncertain significance (Sep 26, 2023)
16-77735940-C-G		not specified	Uncertain significance (Sep 12, 2023)
16-77741600-C-T		not specified	Uncertain significance (Dec 15, 2023)
16-77741601-C-T		not specified	Uncertain significance (Sep 17, 2021)
16-77741621-C-T		not specified	Uncertain significance (Jan 24, 2024)
16-77741623-C-G		not specified	Uncertain significance (Aug 12, 2021)
16-77741706-A-G		not specified	Uncertain significance (Jul 25, 2023)
16-77741726-C-T		not specified	Uncertain significance (Nov 18, 2022)
16-77741739-G-A		not specified	Likely benign (Jun 28, 2022)
16-77741751-A-G		not specified	Uncertain significance (Apr 22, 2022)
16-77741780-G-A		not specified	Uncertain significance (Jul 26, 2022)
16-77741786-A-G		not specified	Uncertain significance (Nov 09, 2023)
16-77741815-C-A		not specified	Likely benign (Jan 24, 2024)
16-77741853-A-T		not specified	Uncertain significance (Jun 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NUDT7	protein_coding	protein_coding	ENST00000268533	4	19747

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.44e-7	0.0947	124503	1	289	124793	0.00116

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.825	164	137	1.20	0.00000754	1540
Missense in Polyphen		53	49.152	1.0783		550
Synonymous	-1.82	68	51.4	1.32	0.00000264	471
Loss of Function	-0.877	8	5.73	1.40	2.46e-7	82

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000629	0.000629
Ashkenazi Jewish	0.00159	0.00159
East Asian	0.0000556	0.0000556
Finnish	0.00139	0.00139
European (Non-Finnish)	0.00192	0.00191
Middle Eastern	0.0000556	0.0000556
South Asian	0.0000344	0.0000327
Other	0.000990	0.000990

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Coenzyme A diphosphatase which mediates the cleavage of CoA, CoA esters and oxidized CoA with similar efficiencies, yielding 3',5'-ADP and the corresponding 4'-phosphopantetheine derivative as products. CoA into 3',5'-ADP and 4'- phosphopantetheine. Has no activity toward NDP-sugars, CDP- alcohols, (deoxy)nucleoside 5'-triphosphates, nucleoside 5'-di or monophosphates, diadenosine polyphosphates, NAD, NADH, NADP, NADPH or thymidine-5'-monophospho-p-nitrophenyl ester. May be required to eliminate oxidized CoA from peroxisomes, or regulate CoA and acyl-CoA levels in this organelle in response to metabolic demand. Does not play a role in U8 snoRNA decapping activity. Binds U8 snoRNA (By similarity). {ECO:0000250}.
• Pathway: Peroxisome - Homo sapiens (human);Metabolism of lipids;Metabolism of proteins;Peroxisomal lipid metabolism;Metabolism;Peroxisomal protein import;Fatty acid metabolism (Consensus)

Recessive Scores

• pRec: 0.0950

Intolerance Scores

• loftool: 0.780
• rvis_EVS: 0.33
• rvis_percentile_EVS: 73.41

Haploinsufficiency Scores

• pHI: 0.102
• hipred: N
• hipred_score: 0.146
• ghis: 0.453

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.228

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nudt7

Gene ontology

• Biological process: protein targeting to peroxisome;biological_process;fatty acid catabolic process;nucleoside diphosphate metabolic process;coenzyme A catabolic process;acetyl-CoA catabolic process;brown fat cell differentiation
• Cellular component: peroxisome;peroxisomal matrix;cytosol
• Molecular function: magnesium ion binding;molecular_function;acetyl-CoA hydrolase activity;signaling receptor binding;CoA hydrolase activity;manganese ion binding;snoRNA binding;m7G(5')pppN diphosphatase activity