ASMTL

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

Basic information

Region (hg38): Y:1403139-1453762

Links

∙ NCBI:8623 ∙ OMIM:300162, 400011 ∙ HGNC:751 ∙ Uniprot:O95671 ∙ 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 ASMTL gene.

Myoepithelial tumor (1 variants)

Variants pathogenicity by type

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

Variants in ASMTL

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

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

Position	Type	Phenotype	Significance	ClinVar
Y-1428032-G-A		Myoepithelial tumor	Uncertain significance (Nov 01, 2022)	1801731

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ASMTL	protein_coding	protein_coding	ENST00000381317	13	50624

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.27e-9	0.792	124487	0	172	124659	0.000690

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.609	444	409	1.08	0.0000277	4012
Missense in Polyphen		134	142.45	0.94066		1436
Synonymous	-1.33	217	193	1.12	0.0000156	1247
Loss of Function	1.57	18	26.8	0.672	0.00000131	298

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000413	0.000413
Ashkenazi Jewish	0.0000999	0.0000993
East Asian	0.000668	0.000668
Finnish	0.00102	0.00102
European (Non-Finnish)	0.000388	0.000381
Middle Eastern	0.000668	0.000668
South Asian	0.00239	0.00239
Other	0.00133	0.00132

dbNSFP

Source: dbNSFP

Function: FUNCTION: Unknown. The presence of the putative catalytic domain of S-adenosyl-L-methionine binding argues for a methyltransferase activity.;

Intolerance Scores

loftool: 0.843
rvis_EVS: 2.17
rvis_percentile_EVS: 98.04

Haploinsufficiency Scores

pHI: 0.0907
hipred: N
hipred_score: 0.253
ghis: 0.411

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.736

Gene Damage Prediction

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

Gene ontology

Biological process: biological_process;methylation
Cellular component: cytosol
Molecular function: molecular_function;protein binding;O-methyltransferase activity;nucleoside-triphosphate diphosphatase activity