NAPRT

nicotinate phosphoribosyltransferase

Basic information

Region (hg38): 8:143574785-143578649

Previous symbols: [ "NAPRT1" ]

Links

ENSG00000147813 ∙ NCBI:93100 ∙ OMIM:611552 ∙ HGNC:30450 ∙ Uniprot:Q6XQN6 ∙ 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 NAPRT gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NAPRT 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	2
missense			54	4		58
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	55	5	1

Variants in NAPRT

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

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

Position	Type	Phenotype	Significance	ClinVar
8-143574869-A-G		not specified	Uncertain significance (Jan 30, 2024)
8-143575011-C-T		not specified	Uncertain significance (Oct 06, 2021)
8-143575032-C-T		not specified	Likely benign (Feb 28, 2023)
8-143575044-A-T		not specified	Likely benign (Jan 03, 2024)
8-143575045-G-T		not specified	Uncertain significance (Oct 04, 2022)
8-143575086-T-C		not specified	Uncertain significance (Aug 12, 2021)
8-143575100-G-C			Benign (Jan 19, 2018)
8-143575213-C-T		not specified	Uncertain significance (Apr 27, 2024)
8-143575244-C-T		not specified	Uncertain significance (Aug 02, 2022)
8-143575330-T-A		not specified	Uncertain significance (Apr 07, 2023)
8-143575330-TC-T			Uncertain significance (May 23, 2022)
8-143575450-C-T		not specified	Uncertain significance (Dec 12, 2023)
8-143575486-C-T		not specified	Uncertain significance (Oct 02, 2023)
8-143575648-G-C		not specified	Uncertain significance (Oct 26, 2022)
8-143576091-C-T		not specified	Uncertain significance (Apr 14, 2022)
8-143576095-C-T		not specified	Uncertain significance (Jun 16, 2023)
8-143576104-C-T		not specified	Uncertain significance (Feb 16, 2023)
8-143576471-G-T		not specified	Uncertain significance (Jan 07, 2022)
8-143576494-G-A			Benign (Jan 19, 2018)
8-143576511-C-T		not specified	Uncertain significance (Dec 09, 2023)
8-143576519-T-C		not specified	Uncertain significance (May 14, 2024)
8-143576550-C-T		not specified	Uncertain significance (Oct 02, 2023)
8-143576558-T-G		not specified	Uncertain significance (Aug 23, 2021)
8-143576656-T-C		not specified	Uncertain significance (Nov 09, 2023)
8-143576685-C-A		not specified	Uncertain significance (Jul 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NAPRT	protein_coding	protein_coding	ENST00000449291	13	3865

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.15e-18	0.00259	125403	0	122	125525	0.000486

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.616	331	301	1.10	0.0000181	3330
Missense in Polyphen		129	116.36	1.1086		1278
Synonymous	-1.21	157	139	1.13	0.00000855	1204
Loss of Function	-0.164	27	26.1	1.03	0.00000150	263

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00118	0.00113
Ashkenazi Jewish	0.00	0.00
East Asian	0.000498	0.000490
Finnish	0.00	0.00
European (Non-Finnish)	0.000557	0.000529
Middle Eastern	0.000498	0.000490
South Asian	0.000772	0.000752
Other	0.000686	0.000653

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the first step in the biosynthesis of NAD from nicotinic acid, the ATP-dependent synthesis of beta-nicotinate D- ribonucleotide from nicotinate and 5-phospho-D-ribose 1-phosphate (PubMed:17604275, PubMed:21742010, PubMed:26042198). Helps prevent cellular oxidative stress via its role in NAD biosynthesis (PubMed:17604275). {ECO:0000269|PubMed:17604275, ECO:0000269|PubMed:21742010, ECO:0000269|PubMed:26042198}.
• Pathway: Nicotinate and nicotinamide metabolism - Homo sapiens (human);NAD+ biosynthetic pathways;Neutrophil degranulation;Innate Immune System;Immune System;Metabolism;Nicotinamide salvaging;Nicotinate metabolism;Metabolism of water-soluble vitamins and cofactors;Metabolism of vitamins and cofactors (Consensus)

Recessive Scores

• pRec: 0.114

Intolerance Scores

• rvis_EVS: -1.02
• rvis_percentile_EVS: 8.1

Haploinsufficiency Scores

• pHI: 0.0603
• hipred: N
• hipred_score: 0.170
• ghis: 0.586

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Naprt

Gene ontology

• Biological process: response to oxidative stress;NAD biosynthetic process;nicotinate nucleotide salvage;NAD salvage;NAD biosynthesis via nicotinamide riboside salvage pathway;neutrophil degranulation
• Cellular component: extracellular region;cytosol;azurophil granule lumen;extracellular exosome
• Molecular function: nicotinate-nucleotide diphosphorylase (carboxylating) activity;nicotinate phosphoribosyltransferase activity;protein binding;metal ion binding