NMNAT3

nicotinamide nucleotide adenylyltransferase 3

Basic information

Region (hg38): 3:139560180-139678017

Links

ENSG00000163864

∙ NCBI:349565 ∙ OMIM:608702 ∙ HGNC:20989 ∙ Uniprot:Q96T66 ∙ 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 NMNAT3 gene.

not_specified (29 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NMNAT3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001401600.1. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			29 clinvar			29
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	29	0	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NMNAT3	protein_coding	protein_coding	ENST00000406164	3	117838

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.24e-8	0.0764	125667	0	81	125748	0.000322

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.159	133	128	1.04	0.00000716	1413
Missense in Polyphen		55	48.628	1.131		575
Synonymous	0.605	45	50.5	0.892	0.00000293	421
Loss of Function	-0.595	10	8.16	1.22	5.21e-7	73

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000366	0.000366
Ashkenazi Jewish	0.00	0.00
East Asian	0.000544	0.000544
Finnish	0.000694	0.000693
European (Non-Finnish)	0.000397	0.000396
Middle Eastern	0.000544	0.000544
South Asian	0.0000387	0.0000327
Other	0.000491	0.000489

dbNSFP

Source: dbNSFP

Function: FUNCTION: Catalyzes the formation of NAD(+) from nicotinamide mononucleotide (NMN) and ATP. Can also use the deamidated form; nicotinic acid mononucleotide (NaMN) as substrate with the same efficiency. Can use triazofurin monophosphate (TrMP) as substrate. Can also use GTP and ITP as nucleotide donors. Also catalyzes the reverse reaction, i.e. the pyrophosphorolytic cleavage of NAD(+). For the pyrophosphorolytic activity, can use NAD(+), NADH, NaAD, nicotinic acid adenine dinucleotide phosphate (NHD), nicotinamide guanine dinucleotide (NGD) as substrates. Fails to cleave phosphorylated dinucleotides NADP(+), NADPH and NaADP(+). Protects against axonal degeneration following injury. {ECO:0000269|PubMed:16118205, ECO:0000269|PubMed:17402747}.;
Pathway: Nicotinate and nicotinamide metabolism - Homo sapiens (human);NAD+ metabolism;Vitamin B3 (nicotinate and nicotinamide) metabolism;Metabolism;Nicotinate metabolism;Metabolism of water-soluble vitamins and cofactors;Metabolism of vitamins and cofactors;NAD salvage;NAD biosynthesis from 2-amino-3-carboxymuconate semialdehyde;NAD <i>de novo</i> biosynthesis;superpathway of tryptophan utilization (Consensus)

Recessive Scores

pRec: 0.133

Intolerance Scores

loftool
rvis_EVS: 0.08
rvis_percentile_EVS: 60.31

Haploinsufficiency Scores

pHI: 0.299
hipred: N
hipred_score: 0.190
ghis: 0.609

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.714

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Nmnat3
Phenotype: homeostasis/metabolism phenotype; immune system phenotype; hematopoietic system phenotype;

Gene ontology

Biological process: NAD biosynthetic process;response to wounding;NAD metabolic process;response to tumor necrosis factor;'de novo' NAD biosynthetic process from aspartate
Cellular component: mitochondrion;mitochondrial matrix;axon;neuronal cell body
Molecular function: nicotinamide-nucleotide adenylyltransferase activity;nicotinate-nucleotide adenylyltransferase activity;ATP binding