N6AMT1

N-6 adenine-specific DNA methyltransferase 1, the group of 7BS protein methyltransferases

Basic information

Region (hg38): 21:28872191-28885371

Previous symbols: [ "C21orf127", "HEMK2" ]

Links

ENSG00000156239

∙ NCBI:29104 ∙ OMIM:614553 ∙ HGNC:16021 ∙ Uniprot:Q9Y5N5 ∙ 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 N6AMT1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the N6AMT1 gene is commonly pathogenic or not. These statistics are base on transcript: . 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						0
missense			28 clinvar	2 clinvar		30
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	28	2	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
N6AMT1	protein_coding	protein_coding	ENST00000303775	6	13181

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000682	0.293	124720	0	1007	125727	0.00401

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.230	123	116	1.06	0.00000549	1349
Missense in Polyphen		28	36.289	0.77158		422
Synonymous	0.0938	43	43.8	0.982	0.00000219	440
Loss of Function	0.0962	8	8.30	0.964	3.47e-7	112

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00705	0.00661
Ashkenazi Jewish	0.000931	0.000893
East Asian	0.00447	0.00370
Finnish	0.0167	0.0162
European (Non-Finnish)	0.00368	0.00343
Middle Eastern	0.00447	0.00370
South Asian	0.000445	0.000425
Other	0.00287	0.00261

dbNSFP

Source: dbNSFP

Function: FUNCTION: Methyltransferase that can methylate both proteins and DNA, and to a lower extent, arsenic (PubMed:18539146, PubMed:21193388, PubMed:30017583). Catalytic subunit of a heterodimer with TRMT112, which catalyzes N5-methylation of Glu residue of proteins with a Gly-Gln-Xaa-Xaa-Xaa-Arg motif (PubMed:18539146) (By similarity). Methylates ETF1 on 'Gln-185'; ETF1 needs to be complexed to ERF3 in its GTP-bound form to be efficiently methylated (PubMed:18539146, PubMed:20606008). Also acts as a N(6)-adenine-specific DNA methyltransferase by mediating methylation of DNA on the 6th position of adenine (N(6)- methyladenosine) (PubMed:30017583). N(6)-methyladenosine (m6A) DNA is significantly enriched in exonic regions and is associated with gene transcriptional activation (PubMed:30017583). May also play a role in the modulation of arsenic-induced toxicity by mediating the conversion of monomethylarsonous acid (3+) into the less toxic dimethylarsonic acid (PubMed:21193388, PubMed:25997655). It however only plays a limited role in arsenic metabolism compared with AS3MT (PubMed:25997655). {ECO:0000250|UniProtKB:Q6SKR2, ECO:0000269|PubMed:18539146, ECO:0000269|PubMed:20606008, ECO:0000269|PubMed:21193388, ECO:0000269|PubMed:25997655, ECO:0000269|PubMed:30017583}.;
Pathway: Methylation;Phase II - Conjugation of compounds;Eukaryotic Translation Termination;Translation;Metabolism of proteins;Biological oxidations;Metabolism (Consensus)

Recessive Scores

pRec: 0.0959

Intolerance Scores

loftool
rvis_EVS: 0.73
rvis_percentile_EVS: 86.08

Haploinsufficiency Scores

pHI: 0.490
hipred: N
hipred_score: 0.292
ghis: 0.420

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: E
essential_gene_gene_trap: E
gene_indispensability_pred: N
gene_indispensability_score: 0.464

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: N6amt1
Phenotype: growth/size/body region phenotype; embryo 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);

Gene ontology

Biological process: toxin metabolic process;peptidyl-glutamine methylation;arsonoacetate metabolic process;positive regulation of cell growth;methylation;DNA methylation on adenine
Cellular component: nucleus;cytosol;protein-containing complex;eRF1 methyltransferase complex
Molecular function: nucleic acid binding;protein binding;protein methyltransferase activity;S-adenosylmethionine-dependent methyltransferase activity;site-specific DNA-methyltransferase (adenine-specific) activity;methylarsonite methyltransferase activity;protein-glutamine N-methyltransferase activity