NTMT1

N-terminal Xaa-Pro-Lys N-methyltransferase 1, the group of 7BS protein methyltransferases

Basic information

Region (hg38): 9:129608884-129636135

Previous symbols: [ "C9orf32", "METTL11A" ]

Links

ENSG00000148335 ∙ NCBI:28989 ∙ OMIM:613560 ∙ HGNC:23373 ∙ Uniprot:Q9BV86 ∙ 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 NTMT1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NTMT1 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			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	0	0

Variants in NTMT1

This is a list of pathogenic ClinVar variants found in the NTMT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-129613552-G-A		not specified	Likely benign (Jul 06, 2021)
9-129619764-T-C			Likely benign (Feb 01, 2023)
9-129620195-G-A		not specified	Uncertain significance (Sep 09, 2021)
9-129620377-G-A			Likely benign (Feb 01, 2023)
9-129632763-G-T		not specified	Uncertain significance (Sep 04, 2024)
9-129632772-C-G		not specified	Uncertain significance (Apr 07, 2022)
9-129632788-G-A		not specified	Uncertain significance (Dec 31, 2024)
9-129632797-G-T		not specified	Uncertain significance (Sep 04, 2024)
9-129632839-C-T		not specified	Uncertain significance (Nov 09, 2022)
9-129632840-G-A		not specified	Uncertain significance (Nov 26, 2024)
9-129634096-G-C		not specified	Uncertain significance (Feb 25, 2025)
9-129634123-C-T		not specified	Uncertain significance (Jan 22, 2024)
9-129634196-C-T		not specified	Uncertain significance (Oct 25, 2022)
9-129635357-G-A		not specified	Uncertain significance (Oct 02, 2023)
9-129635367-G-A		not specified	Uncertain significance (Oct 18, 2021)
9-129635373-T-A		not specified	Uncertain significance (Nov 21, 2024)
9-129635378-A-G		not specified	Uncertain significance (Nov 15, 2024)
9-129635397-T-G		not specified	Uncertain significance (Dec 28, 2023)
9-129635439-A-G		not specified	Uncertain significance (Oct 06, 2022)
9-129635445-A-G		not specified	Uncertain significance (Dec 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NTMT1	protein_coding	protein_coding	ENST00000372486	3	27047

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0508	0.868	125735	0	12	125747	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.29	104	148	0.702	0.00000954	1479
Missense in Polyphen		38	64.986	0.58474		650
Synonymous	-0.670	75	68.0	1.10	0.00000525	435
Loss of Function	1.45	3	7.19	0.417	3.04e-7	85

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000904	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000533	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Distributive alpha-N-methyltransferase that methylates the N-terminus of target proteins containing the N-terminal motif [Ala/Gly/Pro/Ser]-Pro-Lys when the initiator Met is cleaved. Specifically catalyzes mono-, di- or tri-methylation of the exposed alpha-amino group of the Ala, Gly or Ser residue in the [Ala/Gly/Ser]-Pro-Lys motif and mono- or di-methylation of Pro in the Pro-Pro-Lys motif. Some of the substrates may be primed by METTL11B-mediated monomethylation (PubMed:24090352). Catalyzes the trimethylation of the N-terminal Gly in CENPA (after removal of Met-1). Responsible for the N-terminal methylation of KLHL31, MYL2, MYL3, RB1, RCC1, RPL23A and SET. Required during mitosis for normal bipolar spindle formation and chromosome segregation via its action on RCC1. {ECO:0000269|PubMed:20481588, ECO:0000269|PubMed:20668449, ECO:0000269|PubMed:24090352, ECO:0000269|PubMed:26543159}.

Recessive Scores

• pRec: 0.124

Intolerance Scores

• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.09

Haploinsufficiency Scores

• pHI: 0.171
• hipred: Y
• hipred_score: 0.601
• ghis: 0.615

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ntmt1
• Phenotype: skeleton phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); reproductive 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); liver/biliary system phenotype; cellular phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan)

Gene ontology

• Biological process: spindle organization;chromosome segregation;histone methylation;N-terminal peptidyl-alanine trimethylation;N-terminal peptidyl-glycine methylation;N-terminal peptidyl-proline dimethylation;N-terminal peptidyl-serine dimethylation;N-terminal peptidyl-serine trimethylation
• Cellular component: nucleus;nucleoplasm;cytoplasm;cytosol
• Molecular function: protein binding;protein methyltransferase activity;histone methyltransferase activity;N-terminal protein N-methyltransferase activity