NMT1

N-myristoyltransferase 1

Basic information

Region (hg38): 17:44957992-45109016

Links

ENSG00000136448 ∙ NCBI:4836 ∙ OMIM:160993 ∙ HGNC:7857 ∙ Uniprot:P30419 ∙ 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 NMT1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NMT1 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			36			36
Total	0	0	49	0	0

Variants in NMT1

This is a list of pathogenic ClinVar variants found in the NMT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-44960201-A-G		not specified	Uncertain significance (May 23, 2023)
17-44960289-C-G		not specified	Uncertain significance (Dec 19, 2023)
17-44960310-T-C		not specified	Uncertain significance (Jul 25, 2023)
17-44967634-G-T		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
17-44967669-A-C		not specified	Uncertain significance (Aug 13, 2021)
17-44967700-C-A		not specified	Uncertain significance (Jun 17, 2024)
17-44967705-C-T		not specified	Uncertain significance (Apr 25, 2023)
17-44967711-G-A		not specified	Uncertain significance (May 31, 2023)
17-44967723-C-T		not specified	Uncertain significance (Oct 05, 2023)
17-44967733-C-G		not specified	Uncertain significance (Sep 25, 2023)
17-44967793-C-A		not specified	Uncertain significance (Jul 06, 2021)
17-44967823-C-T		not specified	Uncertain significance (Aug 15, 2023)
17-44967853-G-C		not specified	Uncertain significance (Mar 20, 2023)
17-44967870-G-C		not specified	Uncertain significance (Sep 20, 2023)
17-44967912-G-A		not specified	Uncertain significance (May 26, 2024)
17-44967925-C-T		not specified	Uncertain significance (Feb 13, 2023)
17-44967996-G-A		not specified	Uncertain significance (Oct 05, 2023)
17-45024488-G-A		not specified	Uncertain significance (Aug 12, 2021)
17-45024489-C-T		not specified	Uncertain significance (Aug 12, 2021)
17-45024518-G-A		not specified	Uncertain significance (Nov 18, 2022)
17-45024537-G-A		not specified	Uncertain significance (Nov 10, 2023)
17-45024552-G-A		not specified	Uncertain significance (May 13, 2024)
17-45024611-C-T		not specified	Uncertain significance (Aug 12, 2021)
17-45024674-C-T		not specified	Uncertain significance (Jul 16, 2021)
17-45024690-G-A		not specified	Uncertain significance (Nov 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NMT1	protein_coding	protein_coding	ENST00000592782	12	57407

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.996	0.00450	125744	0	4	125748	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.48	173	292	0.592	0.0000165	3297
Missense in Polyphen		19	90.678	0.20953		1005
Synonymous	0.352	107	112	0.958	0.00000645	928
Loss of Function	4.49	3	29.2	0.103	0.00000175	304

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.00000879	0.00000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Adds a myristoyl group to the N-terminal glycine residue of certain cellular and viral proteins. {ECO:0000269|PubMed:25255805, ECO:0000269|PubMed:9353336, ECO:0000269|PubMed:9506952}.
• Pathway: Signaling by GPCR;Disease;Signal Transduction;Late Phase of HIV Life Cycle;HIV Life Cycle;HIV Infection;Intrinsic Pathway for Apoptosis;Infectious disease;Apoptosis;Programmed Cell Death;Activation, myristolyation of BID and translocation to mitochondria;G alpha (i) signalling events;Inactivation, recovery and regulation of the phototransduction cascade;The phototransduction cascade;Visual phototransduction;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.0670
• rvis_EVS: -0.56
• rvis_percentile_EVS: 19.31

Haploinsufficiency Scores

• pHI: 0.603
• hipred: Y
• hipred_score: 0.783
• ghis: 0.646

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.959

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nmt1
• Phenotype: immune system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; cellular phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: in utero embryonic development;N-terminal protein myristoylation;N-terminal peptidyl-glycine N-myristoylation;regulation of rhodopsin mediated signaling pathway;cellular ketone metabolic process;positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway
• Cellular component: cytoplasm;mitochondrion;cytosol;plasma membrane;extrinsic component of membrane
• Molecular function: glycylpeptide N-tetradecanoyltransferase activity;myristoyltransferase activity