NNMT

nicotinamide N-methyltransferase, the group of 7BS small molecule methyltransferases

Basic information

Region (hg38): 11:114257787-114313536

Links

ENSG00000166741NCBI:4837OMIM:600008HGNC:7861Uniprot:P40261AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NNMT 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
19
clinvar
1
clinvar
20
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 19 1 0

Variants in NNMT

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

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

Position Type Phenotype Significance ClinVar
11-114296598-T-A not specified Uncertain significance (Dec 15, 2022)2366488
11-114296608-C-T not specified Uncertain significance (Feb 27, 2023)2463523
11-114296609-G-A not specified Uncertain significance (Feb 22, 2023)2471407
11-114296675-A-C not specified Uncertain significance (May 02, 2024)3300188
11-114297953-G-T not specified Uncertain significance (Feb 16, 2023)2459847
11-114297962-G-A not specified Uncertain significance (Feb 17, 2024)3200877
11-114298002-A-G not specified Uncertain significance (Jun 10, 2024)3300185
11-114298007-C-A not specified Uncertain significance (Jul 06, 2021)2235157
11-114298062-A-C not specified Uncertain significance (Nov 14, 2023)3200878
11-114298146-T-C not specified Uncertain significance (Feb 03, 2022)2215256
11-114312160-G-A not specified Uncertain significance (Dec 12, 2023)3200879
11-114312160-G-C not specified Likely benign (Sep 16, 2021)2388562
11-114312173-T-C not specified Uncertain significance (Jan 30, 2024)3200880
11-114312187-G-A not specified Uncertain significance (Feb 15, 2023)2463418
11-114312198-C-A not specified Uncertain significance (Feb 28, 2024)3200881
11-114312218-C-T not specified Uncertain significance (Dec 15, 2022)3200882
11-114312228-C-A not specified Uncertain significance (Aug 03, 2022)2355184
11-114312242-T-A not specified Uncertain significance (Nov 17, 2022)2225674
11-114312242-T-G not specified Uncertain significance (Mar 19, 2024)3300187
11-114312295-A-G not specified Uncertain significance (Feb 15, 2023)2485335
11-114312334-C-T not specified Uncertain significance (Oct 03, 2022)2319489
11-114312335-G-A not specified Uncertain significance (Aug 23, 2021)2246816
11-114312452-C-T not specified Uncertain significance (May 03, 2023)2507749

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
NNMTprotein_codingprotein_codingENST00000535401 355499
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
5.28e-80.06941256940531257470.000211
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-1.191881471.280.000008011721
Missense in Polyphen6543.971.4783598
Synonymous-0.6827366.01.110.00000407534
Loss of Function-0.665107.971.253.35e-7108

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0007220.000722
Ashkenazi Jewish0.00009930.0000992
East Asian0.00005520.0000544
Finnish0.000.00
European (Non-Finnish)0.0002570.000255
Middle Eastern0.00005520.0000544
South Asian0.00006530.0000653
Other0.0003260.000326

dbNSFP

Source: dbNSFP

Function
FUNCTION: Catalyzes the N-methylation of nicotinamide and other pyridines to form pyridinium ions. This activity is important for biotransformation of many drugs and xenobiotic compounds.;
Pathway
Nicotinate and nicotinamide metabolism - Homo sapiens (human);Nicotinate and Nicotinamide Metabolism;Metapathway biotransformation Phase I and II;Methylation Pathways;Methylation;Phase II - Conjugation of compounds;Metabolism of amino acids and derivatives;Biological oxidations;Metabolism;Nicotinate Nicotinamide metabolism;Nicotinamide salvaging;Nicotinate metabolism;Selenoamino acid metabolism;Metabolism of water-soluble vitamins and cofactors;Metabolism of vitamins and cofactors;Metabolism of ingested SeMet, Sec, MeSec into H2Se (Consensus)

Recessive Scores

pRec
0.202

Intolerance Scores

loftool
0.620
rvis_EVS
-0.47
rvis_percentile_EVS
23.25

Haploinsufficiency Scores

pHI
0.471
hipred
N
hipred_score
0.241
ghis
0.562

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.981

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Nnmt
Phenotype

Gene ontology

Biological process
response to organonitrogen compound;animal organ regeneration;methylation;NAD biosynthesis via nicotinamide riboside salvage pathway;response to drug
Cellular component
cytoplasm;cytosol
Molecular function
nicotinamide N-methyltransferase activity;pyridine N-methyltransferase activity