ASMTL
protein-codingacetylserotonin O-methyltransferase like, the group of Pseudoautosomal region 1|7BS small molecule methyltransferases
Gene summary
The protein encoded by this gene has an N-terminus that is similar to the multicopy associated filamentation (maf) protein of Bacillus subtilis and to orfE of Escherichia coli, while the C-terminus is similar to N-acetylserotonin O-methyltransferase. This gene is located in the pseudoautosomal region 1 (PAR1) of X and Y chromosomes. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2010]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~50.6 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to ASMTL variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript . Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 1 | 1 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 1 | 0 | 0 | 1 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| Ensembl | ENSP00000370718.3 | 13 | MANE Select | |
| RefSeq | NP_001166944.1 | 24 | Standard | |
| RefSeq | NP_001166945.1 | 24 | Standard | |
| RefSeq | NP_004183.2 | 26 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- biological_process
- methylation
Molecular Function
- molecular_function
- protein binding
- O-methyltransferase activity
- nucleoside-triphosphate diphosphatase activity
Cellular Component
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000381317
- Coding exons
- 13
- Length
- 50624
- Individuals with no LoFs
- 124487
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 172
- Defined
- 124659
- p
- 0.000690
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.609 | 444 | 409 | 1.08 | 0.0000277 | 4012 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000065 | 0.000065 | rare |
| Latino/Admixed American | 0.00035 | 0.00035 | rare |
| Ashkenazi Jewish | 0.00010 | 0.000099 | rare |
| East Asian | 0.00067 | 0.00067 | rare |
| Finnish | 0.0010 | 0.0010 | notable |
| European (Non-Finnish) | 0.00039 | 0.00038 | rare |
| South Asian | 0.0024 | 0.0024 | notable |
| Other | 0.0013 | 0.0013 | notable |
dbNSFP Gene Annotations
Source:
- 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
Essentials
- Essential (CRISPR)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.736
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |