NMT2

N-myristoyltransferase 2

Basic information

Region (hg38): 10:15102583-15168693

Links

ENSG00000152465 ∙ NCBI:9397 ∙ OMIM:603801 ∙ HGNC:7858 ∙ Uniprot:O60551 ∙ 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 NMT2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NMT2 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			26	1		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	1	0

Variants in NMT2

This is a list of pathogenic ClinVar variants found in the NMT2 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-15103343-G-A		not specified	Uncertain significance (Aug 16, 2022)
10-15103360-A-G		not specified	Uncertain significance (Jan 19, 2022)
10-15103389-G-C		not specified	Uncertain significance (Jan 25, 2024)
10-15103416-C-A		not specified	Uncertain significance (Aug 01, 2022)
10-15103429-G-A		not specified	Uncertain significance (Aug 02, 2021)
10-15103441-T-G		not specified	Uncertain significance (Jan 23, 2023)
10-15103496-A-C		not specified	Uncertain significance (May 29, 2024)
10-15103544-G-A		not specified	Uncertain significance (Apr 07, 2022)
10-15103604-C-G		not specified	Likely benign (Dec 01, 2022)
10-15103606-A-C		not specified	Uncertain significance (May 06, 2022)
10-15103616-T-C		not specified	Likely benign (Nov 17, 2023)
10-15103696-G-A		not specified	Uncertain significance (Oct 05, 2023)
10-15103714-G-T		not specified	Uncertain significance (Jun 28, 2022)
10-15103735-G-A		not specified	Uncertain significance (Jul 12, 2022)
10-15103761-G-T		not specified	Uncertain significance (Apr 12, 2022)
10-15103764-A-T		not specified	Uncertain significance (Aug 13, 2021)
10-15103801-C-T		not specified	Uncertain significance (Feb 06, 2023)
10-15103804-C-T		not specified	Uncertain significance (Jun 05, 2024)
10-15103811-A-G		not specified	Uncertain significance (Oct 26, 2021)
10-15103825-G-A		not specified	Uncertain significance (Oct 12, 2021)
10-15103999-A-G		not specified	Uncertain significance (Apr 26, 2024)
10-15104060-G-C		not specified	Uncertain significance (Jan 23, 2023)
10-15104080-T-C			Benign (Feb 26, 2018)
10-15104151-A-T		not specified	Uncertain significance (Jan 08, 2024)
10-15109205-A-G		not specified	Uncertain significance (Apr 04, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NMT2	protein_coding	protein_coding	ENST00000378165	12	66110

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.236	0.764	125731	0	16	125747	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.61	200	275	0.727	0.0000147	3266
Missense in Polyphen		70	110.02	0.63626		1406
Synonymous	0.752	102	112	0.910	0.00000674	921
Loss of Function	3.82	7	29.3	0.239	0.00000154	344

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000293	0.0000293
Ashkenazi Jewish	0.00	0.00
East Asian	0.000330	0.000326
Finnish	0.000185	0.000185
European (Non-Finnish)	0.0000178	0.0000176
Middle Eastern	0.000330	0.000326
South Asian	0.0000998	0.0000980
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:9506952}.
• Pathway: Signaling by GPCR;Disease;Signal Transduction;Assembly Of The HIV Virion;Late Phase of HIV Life Cycle;HIV Life Cycle;HIV Infection;Infectious disease;Membrane binding and targetting of GAG proteins;Synthesis And Processing Of GAG, GAGPOL Polyproteins;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: 0.0922

Intolerance Scores

• loftool: 0.643
• rvis_EVS: -0.21
• rvis_percentile_EVS: 38.58

Haploinsufficiency Scores

• pHI: 0.106
• hipred: Y
• hipred_score: 0.704
• ghis: 0.526

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.230

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nmt2
• Phenotype: immune system phenotype; hematopoietic system phenotype; homeostasis/metabolism phenotype; cellular phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: N-terminal peptidyl-glycine N-myristoylation;regulation of rhodopsin mediated signaling pathway;intracellular transport of virus
• Cellular component: cytoplasm;Golgi apparatus;cytosol;plasma membrane;extrinsic component of membrane;host cell
• Molecular function: glycylpeptide N-tetradecanoyltransferase activity