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.

not_specified (28 variants)

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. These statistics are base on transcript: NM_000021079.5. 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				1 clinvar		1
missense			27 clinvar			27
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	27	1	0

Loading clinvar variants...

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
essential_gene_gene_trap
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