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.

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.

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			13			13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	0	0

Variants in NMNAT3

This is a list of pathogenic ClinVar variants found in the NMNAT3 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-139561095-G-A		not specified	Uncertain significance (May 30, 2024)
3-139561161-G-A		not specified	Uncertain significance (Sep 01, 2021)
3-139561293-T-C		not specified	Uncertain significance (Jan 22, 2024)
3-139561317-G-A		not specified	Uncertain significance (Jan 10, 2023)
3-139561359-T-C		not specified	Uncertain significance (Jul 20, 2022)
3-139561360-C-T		not specified	Uncertain significance (Jun 29, 2023)
3-139573668-G-T		not specified	Uncertain significance (Mar 29, 2022)
3-139578887-G-C		not specified	Uncertain significance (Feb 11, 2022)
3-139578894-T-C		not specified	Uncertain significance (Oct 29, 2021)
3-139578906-G-T		not specified	Uncertain significance (Jun 21, 2022)
3-139578929-C-T		not specified	Uncertain significance (Oct 20, 2023)
3-139578969-C-T		not specified	Uncertain significance (Dec 17, 2023)
3-139578974-C-T		not specified	Uncertain significance (Jun 13, 2023)
3-139578990-C-T		not specified	Uncertain significance (Jan 06, 2023)

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

• 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