NUDT14

nudix hydrolase 14, the group of Nudix hydrolase family

Basic information

Region (hg38): 14:105172938-105181323

Links

ENSG00000183828 ∙ NCBI:256281 ∙ OMIM:609219 ∙ HGNC:20141 ∙ Uniprot:O95848 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 8.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
NM_177533.5	NP_803877.2	5	yes	-
ENST00000392568.7	ENSP00000376349.2	5	yes	-
NM_001318380.2	NP_001305309.1	5	-	-
ENST00000546553.1	ENSP00000447933.1	3	-	-

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NUDT14 gene.

• not_specified (41 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NUDT14 gene is commonly pathogenic or not. These statistics are base on transcript: NM_177533.5. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			40	2		42
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3			3
Total	0	0	43	3	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NUDT14	protein_coding	protein_coding	ENST00000392568	5	8386

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		124983	0	22	125005	0.0000880

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0316	127	126	1.01	0.00000809	1389
Missense in Polyphen		46	48.802	0.94258		556
Synonymous	0.192	52	53.8	0.967	0.00000341	484
Loss of Function	0.251	7	7.75	0.903	3.32e-7	101

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000289	0.000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000804	0.0000800
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
Other	0.000164	0.000164

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Hydrolyzes UDP-glucose to glucose 1-phosphate and UMP and ADP-ribose to ribose 5-phosphate and AMP. The physiological substrate is probably UDP-glucose. Poor activity on other substrates such as ADP-glucose, CDP-glucose, GDP-glucose and GDP- mannose.
• Pathway: Post-translational protein modification;Metabolism of proteins;Synthesis of dolichyl-phosphate-glucose;Synthesis of substrates in N-glycan biosythesis;Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein;Asparagine N-linked glycosylation (Consensus)

Recessive Scores

• pRec: 0.117

Intolerance Scores

• loftool: 0.583
• rvis_EVS: -0.36
• rvis_percentile_EVS: 28.93

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.363

Gene Damage Prediction

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

Gene ontology

• Biological process: nucleoside phosphate metabolic process;protein N-linked glycosylation via asparagine;ribose phosphate metabolic process
• Cellular component: cytosol
• Molecular function: protein binding;UDP-sugar diphosphatase activity;identical protein binding;metal ion binding;ADP-ribose diphosphatase activity