NNMT

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

Basic information

Region (hg38): 11:114257787-114313536

Links

ENSG00000166741 ∙ NCBI:4837 ∙ OMIM:600008 ∙ HGNC:7861 ∙ Uniprot:P40261 ∙ 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 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	1		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)
11-114296608-C-T		not specified	Uncertain significance (Feb 27, 2023)
11-114296609-G-A		not specified	Uncertain significance (Feb 22, 2023)
11-114296632-A-G		not specified	Uncertain significance (Aug 27, 2024)
11-114296675-A-C		not specified	Uncertain significance (May 02, 2024)
11-114297953-G-T		not specified	Uncertain significance (Feb 16, 2023)
11-114297962-G-A		not specified	Uncertain significance (Feb 17, 2024)
11-114298002-A-G		not specified	Uncertain significance (Jun 10, 2024)
11-114298007-C-A		not specified	Uncertain significance (Jul 06, 2021)
11-114298062-A-C		not specified	Uncertain significance (Nov 14, 2023)
11-114298146-T-C		not specified	Uncertain significance (Feb 03, 2022)
11-114312103-T-A		not specified	Uncertain significance (Nov 21, 2024)
11-114312160-G-A		not specified	Uncertain significance (Dec 12, 2023)
11-114312160-G-C		not specified	Likely benign (Sep 16, 2021)
11-114312173-T-C		not specified	Uncertain significance (Jan 30, 2024)
11-114312187-G-A		not specified	Uncertain significance (Feb 15, 2023)
11-114312198-C-A		not specified	Uncertain significance (Feb 28, 2024)
11-114312218-C-T		not specified	Uncertain significance (Dec 15, 2022)
11-114312228-C-A		not specified	Uncertain significance (Aug 03, 2022)
11-114312242-T-A		not specified	Uncertain significance (Nov 17, 2022)
11-114312242-T-G		not specified	Uncertain significance (Mar 19, 2024)
11-114312274-G-A		not specified	Uncertain significance (Dec 03, 2024)
11-114312295-A-G		not specified	Uncertain significance (Feb 15, 2023)
11-114312334-C-T		not specified	Uncertain significance (Oct 03, 2022)
11-114312335-G-A		not specified	Uncertain significance (Aug 23, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NNMT	protein_coding	protein_coding	ENST00000535401	3	55499

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.28e-8	0.0694	125694	0	53	125747	0.000211

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.19	188	147	1.28	0.00000801	1721
Missense in Polyphen		65	43.97	1.4783		598
Synonymous	-0.682	73	66.0	1.11	0.00000407	534
Loss of Function	-0.665	10	7.97	1.25	3.35e-7	108

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000722	0.000722
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.0000552	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000257	0.000255
Middle Eastern	0.0000552	0.0000544
South Asian	0.0000653	0.0000653
Other	0.000326	0.000326

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

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

Mouse Genome Informatics

• Gene name: Nnmt

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