NTMT2

N-terminal Xaa-Pro-Lys N-methyltransferase 2, the group of MicroRNA protein coding host genes|7BS protein methyltransferases

Basic information

Region (hg38): 1:170145959-170168866

Previous symbols: [ "C1orf184", "METTL11B" ]

Links

ENSG00000203740 ∙ NCBI:149281 ∙ ∙ HGNC:31932 ∙ Uniprot:Q5VVY1 ∙ 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 NTMT2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NTMT2 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			22			22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	0	0

Variants in NTMT2

This is a list of pathogenic ClinVar variants found in the NTMT2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-170146118-G-A		not specified	Uncertain significance (Jul 11, 2023)
1-170146120-G-C		Marfanoid habitus and intellectual disability	Uncertain significance (-)
1-170146144-C-T		not specified	Uncertain significance (Jan 23, 2023)
1-170146159-G-C		not specified	Uncertain significance (Jan 19, 2024)
1-170146161-C-G		not specified	Uncertain significance (May 04, 2022)
1-170146211-G-A		not specified	Uncertain significance (Jun 30, 2022)
1-170160524-T-G		not specified	Uncertain significance (Feb 10, 2022)
1-170160529-G-A		not specified	Uncertain significance (May 02, 2024)
1-170160575-G-C		not specified	Uncertain significance (Dec 21, 2022)
1-170160635-T-C		not specified	Uncertain significance (Sep 07, 2022)
1-170160686-T-C		not specified	Uncertain significance (Jul 25, 2023)
1-170166515-C-T		not specified	Uncertain significance (Oct 06, 2021)
1-170166542-G-A		not specified	Uncertain significance (Dec 07, 2021)
1-170166653-T-A		not specified	Uncertain significance (Jul 05, 2023)
1-170166709-C-T		not specified	Uncertain significance (Jan 23, 2024)
1-170167488-C-G		not specified	Uncertain significance (Jan 23, 2023)
1-170167513-C-T		not specified	Uncertain significance (Mar 14, 2023)
1-170167576-T-A		not specified	Uncertain significance (Aug 03, 2022)
1-170167582-G-A		not specified	Uncertain significance (Jun 17, 2022)
1-170167641-C-T		not specified	Uncertain significance (Sep 01, 2021)
1-170167702-C-T		not specified	Uncertain significance (Dec 15, 2022)
1-170167719-G-A		not specified	Uncertain significance (Mar 02, 2023)
1-170167731-G-A		not specified	Uncertain significance (Jan 26, 2023)
1-170167731-G-C		not specified	Uncertain significance (Jun 10, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NTMT2	protein_coding	protein_coding	ENST00000439373	4	21790

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00442	0.881	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.643	127	149	0.852	0.00000773	1877
Missense in Polyphen		47	57.341	0.81966		713
Synonymous	1.71	40	56.3	0.710	0.00000304	518
Loss of Function	1.34	5	9.44	0.530	4.83e-7	121

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Alpha-N-methyltransferase that methylates the N-terminus of target proteins containing the N-terminal motif [Ala/Pro/Ser]- Pro-Lys when the initiator Met is cleaved. Specifically catalyzes monomethylation of exposed alpha-amino group of Ala or Ser residue in the [Ala/Ser]-Pro-Lys motif and Pro in the Pro-Pro-Lys motif. May activate NTMT1 by priming its substrates for trimethylation. {ECO:0000269|PubMed:24090352}.

Intolerance Scores

• rvis_EVS: 1.66
• rvis_percentile_EVS: 96.23

Haploinsufficiency Scores

• pHI: 0.604

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.198

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mettl11b

Gene ontology

• Biological process: N-terminal protein amino acid methylation
• Cellular component: nucleus;cytoplasm
• Molecular function: N-terminal protein N-methyltransferase activity