NUDT19

nudix hydrolase 19, the group of Nudix hydrolase family

Basic information

Region (hg38): 19:32691821-32713792

Links

ENSG00000213965 ∙ NCBI:390916 ∙ ∙ HGNC:32036 ∙ Uniprot:A8MXV4 ∙ 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 NUDT19 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NUDT19 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				1		1
missense			67	4		71
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	67	5	0

Variants in NUDT19

This is a list of pathogenic ClinVar variants found in the NUDT19 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-32691968-G-A		not specified	Uncertain significance (Feb 07, 2023)
19-32691976-C-A			Likely benign (Jun 01, 2022)
19-32691976-C-T		not specified	Uncertain significance (Aug 26, 2022)
19-32692022-C-A		not specified	Uncertain significance (Dec 11, 2024)
19-32692024-G-C		not specified	Uncertain significance (Aug 16, 2021)
19-32692027-G-A		not specified	Uncertain significance (Mar 03, 2025)
19-32692028-G-A		not specified	Uncertain significance (Nov 07, 2022)
19-32692055-C-T		not specified	Uncertain significance (Jan 20, 2025)
19-32692057-C-G		not specified	Uncertain significance (Mar 30, 2024)
19-32692061-C-G		not specified	Uncertain significance (Sep 24, 2024)
19-32692063-C-T		not specified	Uncertain significance (Jan 18, 2025)
19-32692091-T-A		not specified	Uncertain significance (Jan 04, 2022)
19-32692100-T-G		not specified	Uncertain significance (Jan 04, 2022)
19-32692105-C-T		not specified	Uncertain significance (Jan 30, 2024)
19-32692109-C-T		not specified	Uncertain significance (Sep 02, 2024)
19-32692112-C-G		not specified	Uncertain significance (Feb 12, 2025)
19-32692127-T-C		not specified	Uncertain significance (Jul 02, 2024)
19-32692129-C-T		not specified	Uncertain significance (Jul 05, 2024)
19-32692156-G-A		not specified	Uncertain significance (Nov 25, 2024)
19-32692171-G-A		not specified	Uncertain significance (Feb 16, 2023)
19-32692175-G-C		not specified	Uncertain significance (May 26, 2023)
19-32692178-C-G		not specified	Uncertain significance (Feb 13, 2025)
19-32692196-T-G		not specified	Uncertain significance (Jan 26, 2022)
19-32692201-G-A		not specified	Uncertain significance (Oct 26, 2022)
19-32692202-C-A		not specified	Uncertain significance (Oct 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NUDT19	protein_coding	protein_coding	ENST00000397061	3	21836

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.97e-15	0.000376	124624	0	181	124805	0.000725

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.53	270	176	1.54	0.00000933	2326
Missense in Polyphen		77	50.484	1.5252		657
Synonymous	-3.30	114	77.1	1.48	0.00000416	790
Loss of Function	-2.87	17	8.16	2.08	3.53e-7	106

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00108	0.00102
Ashkenazi Jewish	0.00	0.00
East Asian	0.000480	0.000445
Finnish	0.000160	0.000139
European (Non-Finnish)	0.00120	0.000962
Middle Eastern	0.000480	0.000445
South Asian	0.00125	0.00121
Other	0.000920	0.000825

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Coenzyme A diphosphatase that mediates the hydrolysis of a wide range of CoA esters, including choloyl-CoA and branched- chain fatty-acyl-CoA esters. At low substrate concentrations medium and long-chain fatty-acyl-CoA esters are the primary substrates (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: 0.288

Haploinsufficiency Scores

• pHI: 0.102
• hipred: N
• hipred_score: 0.146
• ghis: 0.472

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.175

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nudt19
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan)

Gene ontology

• Biological process: protein targeting to peroxisome;biological_process;fatty acid catabolic process
• Cellular component: cellular_component;peroxisomal matrix;cytosol
• Molecular function: signaling receptor binding;metal ion binding;acyl-CoA hydrolase activity