GeneBe

NMT2

N-myristoyltransferase 2

Basic information

Region (hg38): 10:15102584-15168693

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.

  • not_specified (54 variants)

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. These statistics are base on transcript: NM_000004808.3. 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.

EffectPLPVUSLBBSum
synonymous
0
missense
53
clinvar
1
clinvar
 54
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 53 1 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
NMT2protein_codingprotein_codingENST00000378165 1266110
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.2360.7641257310161257470.0000636
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.612002750.7270.00001473266
Missense in Polyphen70110.020.636261406
Synonymous0.7521021120.9100.00000674921
Loss of Function3.82729.30.2390.00000154344

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00002930.0000293
Ashkenazi Jewish0.000.00
East Asian0.0003300.000326
Finnish0.0001850.000185
European (Non-Finnish)0.00001780.0000176
Middle Eastern0.0003300.000326
South Asian0.00009980.0000980
Other0.000.00

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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