ASMT

acetylserotonin O-methyltransferase, the group of 7BS small molecule methyltransferases|Pseudoautosomal region 1

Basic information

Region (hg38): X:1615058-1643081

Links

ENSG00000196433 ∙ NCBI:438 ∙ OMIM:300015, 402500 ∙ HGNC:750 ∙ Uniprot:P46597 ∙ 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 ASMT gene.

Variants pathogenicity by type

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

Variants in ASMT

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

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

Position	Type	Phenotype	Significance	ClinVar
X-1615250-C-A		ASMT-related disorder	Conflicting classifications of pathogenicity (Nov 13, 2023)
X-1623156-C-A			Uncertain significance (Dec 15, 2015)
X-1623310-A-G		not specified	Likely benign (Sep 05, 2017)
X-1624390-C-T		ASMT-related disorder	Likely benign (Mar 30, 2021)
X-1629941-T-C			Conflicting classifications of pathogenicity (Jul 31, 2024)
X-1632709-T-C		ASMT-related disorder	Benign (Feb 22, 2023)
X-1632771-C-G		ASMT-related disorder	Likely benign (Aug 10, 2021)
X-1633190-C-A			Uncertain significance (Aug 22, 2019)
X-1633209-G-A		not specified	Uncertain significance (Jul 31, 2024)
X-1636446-T-G			Uncertain significance (Nov 23, 2021)
X-1636511-C-T		ASMT-related disorder	Benign (Feb 16, 2021)
X-1636567-TG-T		ASMT-related disorder	Likely benign (Feb 22, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ASMT	protein_coding	protein_coding	ENST00000381241	9	28081

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.27e-20	0.0000489	125160	1	430	125591	0.00172

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.70	268	200	1.34	0.0000127	2398
Missense in Polyphen		75	60.822	1.2331		732
Synonymous	-2.51	122	91.5	1.33	0.00000716	743
Loss of Function	-2.13	25	15.8	1.58	7.61e-7	196

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00233	0.00233
Ashkenazi Jewish	0.00	0.00
East Asian	0.000603	0.000598
Finnish	0.00402	0.00403
European (Non-Finnish)	0.00225	0.00224
Middle Eastern	0.000603	0.000598
South Asian	0.000653	0.000653
Other	0.00179	0.00180

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Isoform 1 catalyzes the transfer of a methyl group onto N-acetylserotonin, producing melatonin (N-acetyl-5- methoxytryptamine). Isoform 2 and isoform 3 lack enzyme activity. {ECO:0000269|PubMed:22775292}.
• Pathway: Tryptophan metabolism - Homo sapiens (human);Tryptophan Metabolism;Melatonin metabolism and effects;Tryptophan metabolism;Biogenic Amine Synthesis;serotonin and melatonin biosynthesis;Metabolism of amino acids and derivatives;Metabolism;Tryptophan degradation;superpathway of tryptophan utilization;Serotonin and melatonin biosynthesis;Amine-derived hormones (Consensus)

Intolerance Scores

• loftool: 0.969
• rvis_EVS: 0.13
• rvis_percentile_EVS: 63.57

Haploinsufficiency Scores

• pHI: 0.0945
• hipred: N
• hipred_score: 0.170

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.724

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Asmt
• Phenotype: reproductive system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); endocrine/exocrine gland phenotype

Gene ontology

• Biological process: translation;aromatic compound biosynthetic process;melatonin biosynthetic process;methylation;indolalkylamine biosynthetic process
• Cellular component: cytosol
• Molecular function: O-methyltransferase activity;S-methyltransferase activity;S-adenosylmethionine-dependent methyltransferase activity;acetylserotonin O-methyltransferase activity;identical protein binding;protein homodimerization activity