INMT

indolethylamine N-methyltransferase, the group of 7BS small molecule methyltransferases

Basic information

Region (hg38): 7:30697985-30757602

Links

ENSG00000241644 ∙ NCBI:11185 ∙ OMIM:604854 ∙ HGNC:6069 ∙ Uniprot:O95050 ∙ 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 INMT gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the INMT 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					4	4
missense			22	1	1	24
nonsense					1	1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	22	1	6

Variants in INMT

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

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

Position	Type	Phenotype	Significance	ClinVar
7-30752157-G-A		not specified	Uncertain significance (Nov 13, 2023)
7-30752203-G-C		not specified	Uncertain significance (Aug 19, 2024)
7-30752248-C-A		not specified	Uncertain significance (Dec 20, 2022)
7-30752256-G-A		not specified	Uncertain significance (Sep 27, 2024)
7-30752277-G-A		not specified	Uncertain significance (Mar 23, 2022)
7-30752293-C-T		not specified	Uncertain significance (Mar 31, 2024)
7-30753773-C-T		not specified	Uncertain significance (Nov 09, 2024)
7-30753806-C-T		not specified	Uncertain significance (Jun 06, 2023)
7-30753828-C-T			Benign (Jul 15, 2018)
7-30753838-G-A		not specified	Uncertain significance (Dec 01, 2022)
7-30753850-G-A		not specified	Uncertain significance (Jul 12, 2023)
7-30753880-C-A		not specified	Uncertain significance (Aug 04, 2023)
7-30753915-C-T			Benign (Nov 20, 2018)
7-30753916-G-A			Benign (Jul 15, 2018)
7-30755415-T-A			Likely benign (Nov 20, 2018)
7-30755422-C-A		not specified	Uncertain significance (Nov 12, 2021)
7-30755426-C-T			Benign (Jul 31, 2018)
7-30755429-T-C		not specified	Uncertain significance (Sep 14, 2022)
7-30755459-G-A		not specified	Likely benign (Nov 08, 2022)
7-30755468-C-T		not specified	Uncertain significance (May 09, 2023)
7-30755480-T-C		not specified	Uncertain significance (Nov 22, 2023)
7-30755494-G-A			Benign (May 08, 2018)
7-30755550-T-C		not specified	Uncertain significance (Jul 02, 2024)
7-30755561-T-C		not specified	Uncertain significance (Nov 20, 2023)
7-30755585-T-A		not specified	Uncertain significance (Aug 27, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
INMT	protein_coding	protein_coding	ENST00000013222	3	59618

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00332	0.626	125698	0	50	125748	0.000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.358	168	155	1.08	0.00000963	1687
Missense in Polyphen		52	48.941	1.0625		599
Synonymous	-0.922	78	68.3	1.14	0.00000441	541
Loss of Function	0.481	4	5.18	0.772	2.19e-7	67

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00171	0.00171
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000791	0.0000791
Middle Eastern	0.0000544	0.0000544
South Asian	0.000261	0.000261
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions as thioether S-methyltransferase and is active with a variety of thioethers and the corresponding selenium and tellurium compounds, including 3-methylthiopropionaldehyde, dimethyl selenide, dimethyl telluride, 2-methylthioethylamine, 2- methylthioethanol, methyl-n-propyl sulfide and diethyl sulfide. Plays an important role in the detoxification of selenium compounds (By similarity). Catalyzes the N-methylation of tryptamine and structurally related compounds. {ECO:0000250, ECO:0000269|PubMed:10552930}.
• Pathway: Tryptophan metabolism - Homo sapiens (human);Selenocompound metabolism - Homo sapiens (human);Tryptophan Metabolism;Tryptophan metabolism;Methylation Pathways;Methylation of MeSeH for excretion;Metabolism of amino acids and derivatives;Metabolism;Selenoamino acid metabolism;Tryptophan degradation;nicotine degradation IV (Consensus)

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.765
• rvis_EVS: 1.98
• rvis_percentile_EVS: 97.61

Haploinsufficiency Scores

• pHI: 0.109
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.912

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Inmt

Gene ontology

• Biological process: amine metabolic process;response to toxic substance;methylation
• Cellular component: cytoplasm;cytosol
• Molecular function: thioether S-methyltransferase activity;protein binding;amine N-methyltransferase activity;S-adenosyl-L-methionine:beta-alanine N-methyltransferase activity