ASMTL

gene
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Summary

ASMTL (acetylserotonin O-methyltransferase like, HGNC:751) is a protein-coding gene on chromosome Xp22.3 and Yp11.3, encoding Probable bifunctional dTTP/UTP pyrophosphatase/methyltransferase protein (O95671). Nucleoside triphosphate pyrophosphatase that hydrolyzes dTTP and UTP.

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.

Source: NCBI Gene 8623 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 197 total
  • MANE Select transcript: NM_004192

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:751
Approved symbolASMTL
Nameacetylserotonin O-methyltransferase like
LocationXp22.3 and Yp11.3
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000169093
Ensembl biotypeprotein_coding
OMIM300162, 400011
Entrez8623

Gene structure

Transcript identifiers

Ensembl transcripts: 19 — 16 protein_coding, 3 protein_coding_CDS_not_defined

ENST00000381317, ENST00000381333, ENST00000462195, ENST00000463763, ENST00000474865, ENST00000534940, ENST00000861140, ENST00000861141, ENST00000861142, ENST00000861143, ENST00000940599, ENST00000940600, ENST00000940601, ENST00000940602, ENST00000940603, ENST00000940604, ENST00000967039, ENST00000967040, ENST00000967041

RefSeq mRNA: 3 — MANE Select: NM_004192 NM_001173473, NM_001173474, NM_004192

CCDS: CCDS43917, CCDS55362, CCDS55363

Canonical transcript exons

ENST00000381317 — 13 exons

ExonStartEnd
ENSE0000112236114127321412854
ENSE0000112236314179731418116
ENSE0000112237214189821419114
ENSE0000112237814216581421842
ENSE0000112238414255251425687
ENSE0000112239114277341428121
ENSE0000112241214356941435758
ENSE0000228863014031391403489
ENSE0000231329914527481452909
ENSE0000348655214322691432377
ENSE0000350048714350221435083
ENSE0000358045214421861442317
ENSE0000366464014390971439144

Expression profiles

Bgee: expression breadth ubiquitous, 293 present calls, max score 96.46.

Top tissues by expression

295 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
palpebral conjunctivaUBERON:000181296.46gold quality
parotid glandUBERON:000183195.95gold quality
renal glomerulusUBERON:000007494.86gold quality
metanephric glomerulusUBERON:000473694.65gold quality
endothelial cellCL:000011594.63gold quality
parietal pleuraUBERON:000240093.79gold quality
seminal vesicleUBERON:000099893.73gold quality
ponsUBERON:000098893.33gold quality
substantia nigra pars compactaUBERON:000196593.29gold quality
epithelium of nasopharynxUBERON:000195193.28gold quality
corpus epididymisUBERON:000435993.28gold quality
thymusUBERON:000237093.26gold quality
substantia nigra pars reticulataUBERON:000196693.14gold quality
germinal epithelium of ovaryUBERON:000130492.81gold quality
stromal cell of endometriumCL:000225592.54gold quality
synovial jointUBERON:000221792.32gold quality
saphenous veinUBERON:000731892.29gold quality
urethraUBERON:000005792.25gold quality
layer of synovial tissueUBERON:000761692.25gold quality
pleuraUBERON:000097792.19gold quality
middle temporal gyrusUBERON:000277192.15gold quality
metanephrosUBERON:000008191.90gold quality
apex of heartUBERON:000209891.86gold quality
periodontal ligamentUBERON:000826691.83gold quality
caput epididymisUBERON:000435891.82gold quality
penisUBERON:000098991.78gold quality
lateral nuclear group of thalamusUBERON:000273691.75gold quality
kidney epitheliumUBERON:000481991.68gold quality
adenohypophysisUBERON:000219691.67gold quality
popliteal arteryUBERON:000225091.60gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-MTAB-8498yes8.87
E-MTAB-6142no128.06
E-MTAB-6524no118.96
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

6 targeting ASMTL, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-6885-3P99.7570.363187
HSA-MIR-3160-5P99.2869.071938
HSA-MIR-6883-3P97.9767.35643
HSA-MIR-134-5P97.1166.52976
HSA-MIR-311897.1166.58984
HSA-MIR-5579-5P96.3268.54730

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_rerioasmtlENSDARG00000021433
rattus_norvegicusAsmtlENSRNOG00000028166
drosophila_melanogasterCG9515FBGN0032077
caenorhabditis_elegansdod-18WBGENE00008316

Paralogs (1): ASMT (ENSG00000196433)

Protein

Protein identifiers

Probable bifunctional dTTP/UTP pyrophosphatase/methyltransferase proteinO95671 (reviewed: O95671)

All UniProt accessions (1): O95671

UniProt curated annotations — full annotation on UniProt →

Function. Nucleoside triphosphate pyrophosphatase that hydrolyzes dTTP and UTP. Can also hydrolyze CTP and the modified nucleotides pseudo-UTP, 5-methyl-UTP (m(5)UTP) and 5-methyl-CTP (m(5)CTP). Has weak activity with dCTP, 8-oxo-GTP and N(4)-methyl-dCTP. May have a dual role in cell division arrest and in preventing the incorporation of modified nucleotides into cellular nucleic acids. In addition, the presence of the putative catalytic domain of S-adenosyl-L-methionine binding in the C-terminal region argues for a methyltransferase activity.

Subunit / interactions. Homodimer.

Tissue specificity. Widely expressed. In adult, highly expressed in pancreas, placenta, fibroblast, thymus, prostate, testis, ovary and colon. Expressed at lower levels in spleen, small intestine and leukocytes. In fetus, expressed at high levels in the lung and kidney and at lower level in brain and liver.

Cofactor. Pyrophosphatase activity requires a divalent metal cation.

Miscellaneous. The gene coding for this protein is located in the pseudoautosomal region 1 (PAR1) of X and Y chromosomes. It represents a unique fusion product of 2 different genes of different evolutionary origin and function. The N-terminus is homologous to the bacterial maf/orfE genes and the C-terminus is homologous to ASMT. Exon duplication, exon shuffling and gene fusion seem to be common characteristics of the PAR1 region.

Similarity. In the N-terminal section; belongs to the Maf family. YhdE subfamily. In the C-terminal section; belongs to the class I-like SAM-binding methyltransferase superfamily. Cation-independent O-methyltransferase family.

Isoforms (3)

UniProt IDNamesCanonical?
O95671-11yes
O95671-22
O95671-33

RefSeq proteins (5): NP_001166944, NP_001166945, NP_001411122, NP_001411123, NP_004183* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001077COMT_CDomain
IPR003697Maf-likeFamily
IPR012967COMT-like_dimerisationDomain
IPR016461COMT-likeFamily
IPR029001ITPase-like_famHomologous_superfamily
IPR029063SAM-dependent_MTases_sfHomologous_superfamily
IPR036388WH-like_DNA-bd_sfHomologous_superfamily
IPR036390WH_DNA-bd_sfHomologous_superfamily

Pfam: PF00891, PF02545, PF08100

Catalyzed reactions (Rhea), 6 shown:

  • CTP + H2O = CMP + diphosphate + H(+) (RHEA:27762)
  • dTTP + H2O = dTMP + diphosphate + H(+) (RHEA:28534)
  • UTP + H2O = UMP + diphosphate + H(+) (RHEA:29395)
  • 5-methyl-CTP + H2O = 5-methyl-CMP + diphosphate + H(+) (RHEA:58732)
  • 5-methyl-UTP + H2O = 5-methyl-UMP + diphosphate + H(+) (RHEA:58736)
  • psi-UTP + H2O = psi-UMP + diphosphate + H(+) (RHEA:58740)

UniProt features (53 total): mutagenesis site 11, helix 10, strand 8, modified residue 5, region of interest 3, site 3, sequence conflict 3, binding site 3, splice variant 2, sequence variant 2, chain 1, compositionally biased region 1, active site 1

Structure

Experimental structures (PDB)

3 structures.

PDBMethodResolution (Å)
2P5XX-RAY DIFFRACTION2
6XI4X-RAY DIFFRACTION2.22
6XI5X-RAY DIFFRACTION2.61

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O95671-F187.640.75

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (4): 89 (important for substrate specificity; for pyrophosphatase activity); 179 (important for substrate specificity; for pyrophosphatase activity); 88 (proton acceptor; for pyrophosphatase activity); 23 (important for substrate specificity; for pyrophosphatase activity)

Ligand- & substrate-binding residues (3): 482; 508–510; 525

Post-translational modifications (5): 21, 228, 234, 239, 421

Mutagenesis-validated functional residues (11):

PositionPhenotype
19loss of pyrophosphatase activity.
21loss of pyrophosphatase activity.
23decrease in pyrophosphatase activity.
24loss of pyrophosphatase activity.
44loss of pyrophosphatase activity.
57loss of pyrophosphatase activity.
65loss of pyrophosphatase activity.
88loss of pyrophosphatase activity.
99loss of pyrophosphatase activity.
179loss of pyrophosphatase activity.
179strong decrease in pyrophosphatase activity.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 85 (showing top): FAELT_B_CLL_WITH_VH_REARRANGEMENTS_DN, KYNG_DNA_DAMAGE_BY_4NQO, GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, GOBP_NUCLEOBASE_CONTAINING_SMALL_MOLECULE_METABOLIC_PROCESS, RUTELLA_RESPONSE_TO_CSF2RB_AND_IL4_UP, RUTELLA_RESPONSE_TO_HGF_VS_CSF2RB_AND_IL4_DN, ONDER_CDH1_TARGETS_2_UP, SCHLOSSER_SERUM_RESPONSE_DN, HELLER_HDAC_TARGETS_SILENCED_BY_METHYLATION_UP, BASAKI_YBX1_TARGETS_DN, GOBP_METHYLATION, GARY_CD5_TARGETS_UP, BLALOCK_ALZHEIMERS_DISEASE_DN, GOMF_PROTEIN_DIMERIZATION_ACTIVITY, RUTELLA_RESPONSE_TO_HGF_UP

GO Biological Process (2): nucleotide metabolic process (GO:0009117), methylation (GO:0032259)

GO Molecular Function (9): O-methyltransferase activity (GO:0008171), dTTP diphosphatase activity (GO:0036218), UTP diphosphatase activity (GO:0036221), protein dimerization activity (GO:0046983), nucleoside triphosphate diphosphatase activity (GO:0047429), protein binding (GO:0005515), methyltransferase activity (GO:0008168), transferase activity (GO:0016740), hydrolase activity (GO:0016787)

GO Cellular Component (1): cytosol (GO:0005829)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
nucleoside triphosphate diphosphatase activity2
catalytic activity2
nucleoside phosphate metabolic process1
metabolic process1
methyltransferase activity1
protein binding1
pyrophosphatase activity1
binding1
transferase activity, transferring one-carbon groups1
cytoplasm1
cellular anatomical structure1

Protein interactions and networks

STRING

2357 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ASMTLAKAP17AQ02040909
ASMTLSLC25A6P12236885
ASMTLPLCXD1Q9NUJ7743
ASMTLDHRSXQ8N5I4740
ASMTLGTPBP6O43824728
ASMTLNR1I2O75469707
ASMTLZBED1O96006667
ASMTLP2RY8Q86VZ1667
ASMTLSHOXO15266628
ASMTLPPP2R3BQ9Y5P8603
ASMTLEIF1AXP47813574
ASMTLCSF2RAP15509568
ASMTLPUDPQ08623567
ASMTLSPRY3O43610542
ASMTLRBM44Q6ZP01518

IntAct

80 interactions, top by confidence:

ABTypeScore
ASMTLTDO2psi-mi:“MI:0915”(physical association)0.910
TDO2ASMTLpsi-mi:“MI:0915”(physical association)0.910
KRT31ASMTLpsi-mi:“MI:0915”(physical association)0.720
ASMTLKRT31psi-mi:“MI:0915”(physical association)0.720
ASMTLKRT40psi-mi:“MI:0915”(physical association)0.560
ASMTLPNMA1psi-mi:“MI:0915”(physical association)0.560
KRT40ASMTLpsi-mi:“MI:0915”(physical association)0.560
PNMA1ASMTLpsi-mi:“MI:0915”(physical association)0.560
KRT34ASMTLpsi-mi:“MI:0915”(physical association)0.560
ASMTLRELpsi-mi:“MI:0915”(physical association)0.560
ASMTLGORASP2psi-mi:“MI:0915”(physical association)0.560
ASMTLZNF655psi-mi:“MI:0915”(physical association)0.560
ASMTLDCTN1psi-mi:“MI:0915”(physical association)0.560
ASMTLpsi-mi:“MI:0915”(physical association)0.560
OPTNASMTLpsi-mi:“MI:0915”(physical association)0.560

BioGRID (56): ASMTL (Two-hybrid), ASMTL (Two-hybrid), ASMTL (Two-hybrid), PNMA1 (Two-hybrid), KRT40 (Two-hybrid), ASMTL (Two-hybrid), ASMTL (Two-hybrid), ASMTL (Affinity Capture-MS), ASMTL (Affinity Capture-MS), ASMTL (Affinity Capture-MS), ASMTL (Affinity Capture-MS), ASMTL (Affinity Capture-MS), ASMTL (Affinity Capture-MS), ASMTL (Affinity Capture-MS), ASMTL (Affinity Capture-MS)

ESM2 similar proteins: A0JN95, A4IF87, A6NJ78, B5DEQ3, B7ZMP1, D3ZLY0, E9Q4Z2, F1QDI9, G1SPE9, O14717, O15228, O22268, O55055, O95453, O95671, P37287, P69341, P97770, Q05B63, Q08J23, Q0V8R7, Q0VGM9, Q10D00, Q1HFZ0, Q2T9W2, Q4G073, Q5R5T5, Q5R962, Q5R9W8, Q5RC51, Q5RJZ1, Q6GR37, Q6H1L8, Q6NYU2, Q6YJI5, Q7TNK6, Q7YS61, Q7Z4G4, Q8JZM0, Q8R2Y8

Diamond homologs: A0A084R1I1, A0A0N9HMN6, A0A1L9UR19, A0A1W5SMT6, A0A2G5IC53, A0A2S1WC15, A0A2V5HP22, A0A348AXX3, A0A443HJY8, A0A4P8WAD3, A0A7T8J1Z8, A1DA61, A2QBF0, A5ABG3, A9X7L0, B0ZB56, B0ZB57, B1P123, B4XY98, B6VJS4, B8NJH3, B8NY85, B9WZX2, C7SDN9, C9K7C0, D3H5H5, D3KY98, D3KY99, D3KYA0, D7PI16, D7PI18, E7FL15, E9KMQ4, G3XSI5, I1RF60, I3PLQ7, M2YKT1, O24305, O24529, O95671

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

197 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance7
Likely benign3
Benign2

Top pathogenic / likely-pathogenic (0)

SpliceAI

2359 predictions. Top by Δscore:

VariantEffectΔscore
X:1412850:GTCAC:Gacceptor_gain1.0000
X:1412851:TCAC:Tacceptor_gain1.0000
X:1412852:CACC:Cacceptor_gain1.0000
X:1421653:GCTAC:Gdonor_loss1.0000
X:1421654:CTA:Cdonor_loss1.0000
X:1421655:TACCT:Tdonor_loss1.0000
X:1421656:AC:Adonor_loss1.0000
X:1421657:C:CTdonor_loss1.0000
X:1425479:TCC:Tdonor_gain1.0000
X:1425686:CC:Cacceptor_gain1.0000
X:1425686:CCCTG:Cacceptor_loss1.0000
X:1425687:CC:Cacceptor_gain1.0000
X:1425688:C:CCacceptor_gain1.0000
X:1427746:AAAGC:Adonor_gain1.0000
X:1427815:AG:Adonor_gain1.0000
X:1432263:ACTC:Adonor_loss1.0000
X:1432264:CTCA:Cdonor_loss1.0000
X:1432265:TCAC:Tdonor_loss1.0000
X:1432266:CA:Cdonor_loss1.0000
X:1432267:A:ACdonor_gain1.0000
X:1432267:A:Cdonor_loss1.0000
X:1432268:C:CAdonor_gain1.0000
X:1432268:CA:Cdonor_gain1.0000
X:1432268:CAT:Cdonor_gain1.0000
X:1432268:CATG:Cdonor_gain1.0000
X:1432374:TGGT:Tacceptor_gain1.0000
X:1432375:GGTCT:Gacceptor_loss1.0000
X:1432377:TCTG:Tacceptor_loss1.0000
X:1432378:C:CCacceptor_gain1.0000
X:1432378:CT:Cacceptor_loss1.0000

AlphaMissense

8114 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
Y:1439119:A:TV84D0.995
Y:1452771:G:TR24S0.994
Y:1452784:G:CS19R0.993
Y:1452784:G:TS19R0.993
Y:1452786:T:GS19R0.993
Y:1442226:G:TA62D0.992
Y:1428035:A:GF199S0.990
Y:1439116:A:TI85N0.990
Y:1442216:C:AK65N0.990
Y:1442216:C:GK65N0.990
Y:1439111:C:GA87P0.989
Y:1428046:G:CN195K0.988
Y:1428046:G:TN195K0.988
Y:1439107:T:AD88V0.988
Y:1442215:C:GA66P0.988
Y:1442218:T:GK65Q0.988
Y:1442238:G:TA58D0.988
Y:1452788:G:TA18D0.988
Y:1428038:C:TG198E0.987
Y:1439108:C:GD88H0.987
Y:1439113:C:TG86E0.986
Y:1442227:C:GA62P0.986
Y:1452791:A:GL17P0.986
Y:1419004:G:CF452L0.985
Y:1419004:G:TF452L0.985
Y:1419006:A:GF452L0.985
Y:1435048:A:TV125D0.985
Y:1428115:T:AK172N0.983
Y:1428115:T:GK172N0.983
Y:1435051:C:TG124D0.983

dbSNP variants (sampled 300 via entrez): RS111066028 (X:1407046 A>G), RS111066034 (X:1424402 G>A,C), RS111161743 (X:1406777 C>A,G,T), RS111161744 (X:1406789 C>G), RS111161745 (X:1406818 A>G), RS111161747 (X:1416381 A>C), RS111161748 (X:1416385 G>A), RS111161749 (X:1416680 G>A), RS111162408 (X:1416172 T>C,G), RS111162409 (X:1416176 G>A), RS111162410 (X:1416208 A>G), RS111162411 (X:1416248 G>C), RS111162412 (X:1416252 G>A,C), RS111162413 (X:1416315 C>A), RS111162414 (X:1416319 A>G)

Disease associations

OMIM: gene MIM:300162, MIM:400011 | disease phenotypes:

GenCC curated gene-disease

Mondo (2): myoepithelial tumor (MONDO:0002380), primary amenorrhea (MONDO:1060208)

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

MeSH disease descriptors (1)

DescriptorNameTree numbers
D009208MyoepitheliomaC04.557.435.585

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

42 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidincreases expression5
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression, decreases expression2
Decitabineaffects expression, affects cotreatment2
Phenylmercuric Acetateaffects cotreatment, decreases expression2
FR900359increases phosphorylation1
triphenyl phosphateaffects expression1
propionaldehydeincreases expression1
bisphenol Aincreases expression1
trichostatin Aincreases expression1
beta-lapachonedecreases expression1
sodium arsenitedecreases expression1
butyraldehydeincreases expression1
nickel sulfateincreases expression1
coumarinincreases phosphorylation1
pentanalincreases expression1
entinostatincreases expression1
dorsomorphinaffects cotreatment, decreases expression1
LDN 193189affects cotreatment, increases expression1
Sunitinibdecreases expression1
Vorinostataffects cotreatment, affects expression1
Aldehydesincreases expression1
Benzeneincreases expression1
Caffeinedecreases phosphorylation1
Carmustinedecreases expression1
Cisplatinaffects expression1
Copperaffects binding, increases expression1
Disulfiramaffects binding, increases expression1
Estradiolaffects expression1
Ethyl Methanesulfonatedecreases expression1
Folic Aciddecreases expression1

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_SD64HAP1 ASMTL (-) 1Cancer cell lineMale
CVCL_XL60HAP1 ASMTL (-) 2Cancer cell lineMale

Clinical trials (associated diseases)

6 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT03600649PHASE1UNKNOWNClinical Trial of SP-2577 (Seclidemstat) in Patients With Relapsed or Refractory Ewing or Ewing-related Sarcomas
NCT05266196PHASE1/PHASE2UNKNOWNA Rollover Protocol to Allow for Continued Access to the LSD1 Inhibitor Seclidemstat (SP-2577)
NCT06239272PHASE1/PHASE2RECRUITINGNRSTS2021, A Risk Adapted Study Evaluating Maintenance Pazopanib, Limited Margin, Dose-Escalated Radiation Therapy and Selinexor in Non-Rhabdomyosarcoma Soft Tissue Sarcoma (NRSTS)
NCT06625190PHASE1/PHASE2RECRUITINGAlpha/Beta T and B Cell Depletion With Zoledronic Acid for Solid Tumors
NCT06244420Not specifiedCOMPLETEDMalignant Myoepithelioma of Bone and Soft Tissues: Diagnostic Imaging and Histology in Relation to Prognosis
NCT07164248Not specifiedCOMPLETEDEvaluation of Bone Mineral Density Indications and Outcomes in Female Adolescents: Implications for Early Detection of Osteopenia/Osteoporosis and Gynecologic Practice
  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): primary amenorrhea