ASTE1

gene
On this page

Also known as HT001

Summary

ASTE1 (asteroid structure-specific endonuclease 1, HGNC:25021) is a protein-coding gene on chromosome 3q22.1, encoding Single-strand DNA endonuclease ASTE1 (Q2TB18). Structure-specific DNA endonuclease that specifically cleaves single-stranded DNA and 3’ overhang DNA.

Enables 3’ overhang single-stranded DNA endodeoxyribonuclease activity. Involved in double-strand break repair via homologous recombination and double-strand break repair via nonhomologous end joining. Implicated in Lynch syndrome and mismatch repair cancer syndrome.

Source: NCBI Gene 28990 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): palmar fibromatosis (Limited, GenCC)
  • GWAS associations: 2
  • Clinical variants (ClinVar): 111 total
  • MANE Select transcript: NM_014065

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:25021
Approved symbolASTE1
Nameasteroid structure-specific endonuclease 1
Location3q22.1
Locus typegene with protein product
StatusApproved
AliasesHT001
Ensembl geneENSG00000034533
Ensembl biotypeprotein_coding
OMIM620693
Entrez28990

Gene structure

Transcript identifiers

Ensembl transcripts: 18 — 16 protein_coding, 2 nonsense_mediated_decay

ENST00000264992, ENST00000504725, ENST00000504964, ENST00000505290, ENST00000505545, ENST00000507978, ENST00000509060, ENST00000514044, ENST00000874886, ENST00000874887, ENST00000874888, ENST00000874889, ENST00000928636, ENST00000928637, ENST00000928638, ENST00000928639, ENST00000972329, ENST00000972330

RefSeq mRNA: 2 — MANE Select: NM_014065 NM_001288950, NM_014065

CCDS: CCDS3068, CCDS75007

Canonical transcript exons

ENST00000264992 — 6 exons

ExonStartEnd
ENSE00000328922131018506131018716
ENSE00001018068131013875131014387
ENSE00001164451131024005131025331
ENSE00001283678131025474131025594
ENSE00001283683131026507131026825
ENSE00003560577131016144131016339

Expression profiles

Bgee: expression breadth ubiquitous, 233 present calls, max score 88.93.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 6.7543 / max 77.0003, expressed in 1703 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
445856.55641700
445840.195478
445860.00261

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
spermCL:000001988.93gold quality
male germ cellCL:000001587.12gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047382.33gold quality
granulocyteCL:000009481.49gold quality
calcaneal tendonUBERON:000370180.41gold quality
cortical plateUBERON:000534379.23gold quality
rectumUBERON:000105279.00gold quality
mucosa of transverse colonUBERON:000499178.83gold quality
bloodUBERON:000017878.26gold quality
jejunal mucosaUBERON:000039977.89gold quality
ventricular zoneUBERON:000305377.88gold quality
bone marrow cellCL:000209277.36gold quality
tendonUBERON:000004377.33gold quality
small intestine Peyer’s patchUBERON:000345477.26gold quality
amniotic fluidUBERON:000017377.20gold quality
colonic mucosaUBERON:000031777.20gold quality
lymph nodeUBERON:000002977.10gold quality
leukocyteCL:000073876.86gold quality
transverse colonUBERON:000115776.86gold quality
bone marrowUBERON:000237176.80gold quality
ganglionic eminenceUBERON:000402376.75gold quality
small intestineUBERON:000210876.47gold quality
monocyteCL:000057676.37gold quality
mononuclear cellCL:000084276.25gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099176.06gold quality
secondary oocyteCL:000065576.05gold quality
duodenumUBERON:000211475.95gold quality
intestineUBERON:000016075.92gold quality
right lobe of liverUBERON:000111475.86gold quality
large intestineUBERON:000005975.59gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-ANND-3no3.76

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

14 targeting ASTE1, 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-590-3P99.9674.346478
HSA-MIR-3942-3P99.5769.032854
HSA-MIR-5009-3P99.4569.431341
HSA-MIR-302A-5P99.3968.211913
HSA-MIR-510099.1167.521098
HSA-MIR-570198.9769.541502
HSA-MIR-455-3P98.9467.68878
HSA-MIR-541-5P98.2467.771181
HSA-MIR-448398.0964.121642
HSA-MIR-315997.9466.791098
HSA-MIR-89097.4768.67982
HSA-MIR-1910-5P97.4266.36844
HSA-MIR-129396.1664.69916
HSA-MIR-191-5P95.8867.82171

Literature-anchored findings (GeneRIF, showing 4)

  • The four most frequently mutated genes in colorectal cancers with microsatellite instability were ACVR2 (92%), TAF1B (84%), ASTE1/HT001 (80%) and TGFBR2 (77%). (PMID:19503063)
  • Data suggest that calcium ATPase ATP2C1 gene expression is influenced by an overlapping protein asteroid homolog 1 ASTE1 gene. (PMID:23344038)
  • ASTE1 promotes shieldin-complex-mediated DNA repair by attenuating end resection. (PMID:34354233)
  • ASTE1 frameshift mutation triggers the immune response in Epstein-Barr virus-associated gastric cancer. (PMID:34983924)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_rerioASTE1ENSDARG00000062530
mus_musculusAste1ENSMUSG00000032567
rattus_norvegicusAste1ENSRNOG00000013059
drosophila_melanogasterastFBGN0015905

Protein

Protein identifiers

Single-strand DNA endonuclease ASTE1Q2TB18 (reviewed: Q2TB18)

Alternative names: Protein asteroid homolog 1

All UniProt accessions (7): A0A1Y8EM16, Q2TB18, D6R9W5, D6RG30, D6RGH3, D6RJF1, H0Y982

UniProt curated annotations — full annotation on UniProt →

Function. Structure-specific DNA endonuclease that specifically cleaves single-stranded DNA and 3’ overhang DNA. Contributes to the control of DNA double-strand break repair choice by antagonizing BRCA1-dependent homologous recombination (HR) and promoting non-homologous end-joining (NHEJ). Recruited to the single-stranded DNA ends by SHLD2 and cleaves the 3’ exposed DNA ends, therefore inhibiting DNA end resection (necessary for HR) and promoting DNA end protection (necessary for NHEJ).

Subunit / interactions. Interacts with SHLD1, SHLD2, SHLD3, RIF1 and MAD2L2/REV7.

Similarity. Belongs to the asteroid family.

Isoforms (2)

UniProt IDNamesCanonical?
Q2TB18-11yes
Q2TB18-22

RefSeq proteins (2): NP_001275879, NP_054784* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR006085XPG_DNA_repair_NDomain
IPR026832AsteroidFamily
IPR029060PIN-like_dom_sfHomologous_superfamily

Pfam: PF00752

UniProt features (15 total): sequence conflict 8, region of interest 2, splice variant 2, chain 1, compositionally biased region 1, mutagenesis site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q2TB18-F185.400.69

Functional residue map

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

Mutagenesis-validated functional residues (1):

PositionPhenotype
252loss of single-strand dna endonuclease activity.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 89 (showing top): GOMF_ENDONUCLEASE_ACTIVITY, BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN, GOMF_NUCLEASE_ACTIVITY, GOBP_DNA_DAMAGE_RESPONSE, NOUZOVA_TRETINOIN_AND_H4_ACETYLATION, GOBP_RECOMBINATIONAL_REPAIR, chr3q22, GOMF_DNA_ENDONUCLEASE_ACTIVITY, GOBP_DNA_METABOLIC_PROCESS, GOBP_DNA_REPAIR, GOMF_HYDROLASE_ACTIVITY_ACTING_ON_ESTER_BONDS, GOBP_DNA_RECOMBINATION, GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_GREEN_DN, GOMF_SINGLE_STRANDED_DNA_ENDODEOXYRIBONUCLEASE_ACTIVITY, GOMF_CATALYTIC_ACTIVITY_ACTING_ON_DNA

GO Biological Process (3): double-strand break repair via homologous recombination (GO:0000724), double-strand break repair via nonhomologous end joining (GO:0006303), DNA recombination (GO:0006310)

GO Molecular Function (6): single-stranded DNA endonuclease activity (GO:0000014), 3’ overhang single-stranded DNA endonuclease activity (GO:1990599), nuclease activity (GO:0004518), DNA endonuclease activity (GO:0004520), protein binding (GO:0005515), hydrolase activity (GO:0016787)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
double-strand break repair2
recombinational repair1
DNA metabolic process1
DNA endonuclease activity1
hydrolase activity, acting on ester bonds1
single-stranded DNA endonuclease activity1
catalytic activity, acting on a nucleic acid1
endonuclease activity1
DNA nuclease activity1
binding1
catalytic activity1

Protein interactions and networks

STRING

1186 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ASTE1TAF1BQ53T94801
ASTE1USF3Q68DE3513
ASTE1PCNX2A6NKB5474
ASTE1CASP5P51878448
ASTE1POC1BQ8TC44447
ASTE1TUBGCP2Q9BSJ2443
ASTE1ACVR2AP27037436
ASTE1LRTM3Q8NDH2431
ASTE1RIF1Q5UIP0424
ASTE1TGFBR2P37173421
ASTE1AIM2O14862420
ASTE1SLC22A9Q8IVM8389
ASTE1LTN1O94822378
ASTE1FAM161AQ3B820376
ASTE1GAGE12JA6NER3371

IntAct

23 interactions, top by confidence:

ABTypeScore
XRCC4ASTE1psi-mi:“MI:0915”(physical association)0.560
ASTE1XRCC4psi-mi:“MI:0915”(physical association)0.560
ASTE1USP47psi-mi:“MI:0914”(association)0.530
Dctn3psi-mi:“MI:0914”(association)0.350
Mis12psi-mi:“MI:0914”(association)0.350
CDC42BBXpsi-mi:“MI:0914”(association)0.350
ZWINTARHGAP32psi-mi:“MI:0914”(association)0.350
Mtx2NRDCpsi-mi:“MI:0914”(association)0.350
MYH11TBC1D31psi-mi:“MI:0914”(association)0.350
KIF20BACSL3psi-mi:“MI:0914”(association)0.350
GAR1TAF1psi-mi:“MI:0914”(association)0.350
TMEM248TAF1psi-mi:“MI:0914”(association)0.350
Tgs1EFCAB5psi-mi:“MI:0914”(association)0.350
NABP1XPO1psi-mi:“MI:0914”(association)0.350
CDK2MRPL27psi-mi:“MI:0914”(association)0.350
GOLT1Bpsi-mi:“MI:0914”(association)0.350
ZNF692NSD2psi-mi:“MI:0914”(association)0.350
CCDC85ACIBAR1psi-mi:“MI:0914”(association)0.350
ASTE1yopMpsi-mi:“MI:0915”(physical association)0.000

BioGRID (23): ASTE1 (Two-hybrid), ASTE1 (Affinity Capture-MS), ASTE1 (Affinity Capture-MS), ASTE1 (Affinity Capture-MS), ASTE1 (Affinity Capture-MS), ASTE1 (Affinity Capture-MS), ASTE1 (Affinity Capture-MS), ASTE1 (Affinity Capture-MS), ASTE1 (Affinity Capture-MS), ASTE1 (Affinity Capture-MS), ASTE1 (Affinity Capture-MS), ASTE1 (Affinity Capture-MS), ASTE1 (Affinity Capture-MS), ASTE1 (Affinity Capture-MS), USP47 (Affinity Capture-MS)

ESM2 similar proteins: A0A571BF63, A2BF66, A6QQY4, B0BN28, D3ZWE7, E2QXH7, F6RRD7, O02799, O60566, O70481, O95905, P52630, Q05B18, Q0V7M7, Q13257, Q28IH8, Q2KIY6, Q2TB18, Q3B7T8, Q3U1T9, Q3UB74, Q4R8B9, Q5JTW2, Q5M7C8, Q5PQQ9, Q5RA37, Q5RCY5, Q5SQP1, Q5XGL1, Q5XIZ9, Q6IQY5, Q7T0S7, Q86VD1, Q86VS3, Q86X24, Q8C5W4, Q8CDK3, Q8IWV7, Q8IXW5, Q8N7B1

Diamond homologs: Q1LYL8, Q2TB18, Q5RCY5, Q8BIR2

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance96
Likely benign8
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1372 predictions. Top by Δscore:

VariantEffectΔscore
3:131014384:CAGT:Cacceptor_gain1.0000
3:131014388:C:CCacceptor_gain1.0000
3:131016138:GCTTA:Gdonor_loss1.0000
3:131016142:A:ACdonor_gain1.0000
3:131016142:ACCGA:Adonor_loss1.0000
3:131016143:C:CCdonor_gain1.0000
3:131019644:T:TAdonor_gain1.0000
3:131014386:GT:Gacceptor_gain0.9900
3:131014387:TC:Tacceptor_loss0.9900
3:131014388:C:Gacceptor_loss0.9900
3:131014393:C:CTacceptor_gain0.9900
3:131016335:CTTAC:Cacceptor_gain0.9900
3:131016337:TAC:Tacceptor_gain0.9900
3:131016340:CTAA:Cacceptor_loss0.9900
3:131016989:CCTT:Cdonor_gain0.9900
3:131018500:ACCT:Adonor_loss0.9900
3:131018501:CCT:Cdonor_loss0.9900
3:131018502:CTACC:Cdonor_loss0.9900
3:131018503:TAC:Tdonor_loss0.9900
3:131018504:A:ACdonor_gain0.9900
3:131018504:ACCAG:Adonor_loss0.9900
3:131018505:C:CCdonor_gain0.9900
3:131018505:CCAG:Cdonor_loss0.9900
3:131018575:G:Cdonor_gain0.9900
3:131024001:TTACC:Tdonor_loss0.9900
3:131024002:TA:Tdonor_loss0.9900
3:131024004:CCT:Cdonor_gain0.9900
3:131024650:C:CTacceptor_gain0.9900
3:131026505:A:ACdonor_gain0.9900
3:131026506:C:CCdonor_gain0.9900

AlphaMissense

4461 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
3:131016220:A:GW545R0.995
3:131016220:A:TW545R0.995
3:131025303:C:GG2R0.994
3:131025080:A:TV76D0.992
3:131024651:G:TA219E0.990
3:131024824:A:CS161R0.989
3:131024824:A:TS161R0.989
3:131024826:T:GS161R0.989
3:131024188:C:AR373S0.988
3:131024188:C:GR373S0.988
3:131024861:G:TA149D0.988
3:131024821:G:CD162E0.986
3:131024821:G:TD162E0.986
3:131024822:T:AD162V0.986
3:131024822:T:CD162G0.986
3:131024840:A:TV156E0.986
3:131025022:T:AR95S0.986
3:131025022:T:GR95S0.986
3:131024822:T:GD162A0.985
3:131025303:C:AG2C0.985
3:131016189:A:GL555P0.984
3:131024086:C:AR407S0.984
3:131024086:C:GR407S0.984
3:131024769:A:GW180R0.984
3:131024769:A:TW180R0.984
3:131024827:A:CD160E0.984
3:131024827:A:TD160E0.984
3:131025000:C:GA103P0.984
3:131025068:C:TG80E0.984
3:131024189:C:GR373T0.983

dbSNP variants (sampled 300 via entrez): RS1000438403 (3:131018166 G>C), RS1000612831 (3:131017599 G>GAGGTATTA), RS1000684954 (3:131017924 T>A), RS1000723679 (3:131016876 T>C), RS1000776319 (3:131016580 G>A,C,T), RS1000889552 (3:131023256 C>T), RS1000895890 (3:131017346 G>T), RS1000896107 (3:131023780 G>A), RS1001395728 (3:131019842 C>T), RS1001555640 (3:131026482 C>T), RS1002048758 (3:131026212 T>C), RS1002183186 (3:131018003 ATTACTATT>A), RS1002416243 (3:131024270 A>C), RS1002514662 (3:131027518 G>A), RS1002685923 (3:131014062 C>G,T)

Disease associations

OMIM: gene MIM:620693 | disease phenotypes:

GenCC curated gene-disease

DiseaseClassificationInheritance
palmar fibromatosisLimitedAutosomal dominant

Mondo (1): palmar fibromatosis (MONDO:0006345)

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

StudyTraitp-value
GCST005042_7Restless legs syndrome4.000000e-38
GCST008755_11Phenylephrine infusion rate during anesthesia9.000000e-06

MeSH disease descriptors (1)

DescriptorNameTree numbers
D004387Dupuytren ContractureC04.557.450.565.590.340.173; C05.651.197.270; C17.300.270

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

20 total (human), top 20 by PubMed support.

ChemicalActions (top 5)PubMed papers
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamidedecreases expression1
GSK-J4decreases expression1
dicrotophosdecreases expression1
urushioldecreases expression1
triphenyl phosphateaffects expression1
butyraldehydedecreases expression1
di-n-butylphosphoric acidaffects expression1
CGP 52608affects binding, increases reaction1
CPG-oligonucleotidedecreases expression1
Resveratrolincreases expression, affects cotreatment1
Acetaminophenincreases expression1
Air Pollutants, Occupationalaffects expression1
Methyl Methanesulfonateincreases expression1
Plant Extractsaffects cotreatment, increases expression1
Quercetindecreases expression1
Testosteronedecreases expression1
Tretinoindecreases expression1
Cyclosporinedecreases expression1
Aflatoxin B1decreases methylation1
Copper Sulfatedecreases expression1

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

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

CellosaurusNameCategorySex
CVCL_E1R3HAP1 ASTE1 (-) 1Cancer cell lineMale
CVCL_E1R4HAP1 ASTE1 (-) 2Cancer cell lineMale

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT02647619PHASE4COMPLETEDDupuytren´s Disease Study. Primary Disease, MCP Joint, Xiapex, PNF
NCT03000114PHASE4UNKNOWNCollagenase Injection vs Percutaneous Needle Aponeurotomy for Dupuytren’s Disease
NCT03192020PHASE4ACTIVE_NOT_RECRUITINGTrial Comparing Treatment Strategies in Dupuytren’s Contracture
NCT04907812PHASE4UNKNOWNThe Role of Tranexamic Acid in Reducing Post Operative Hand Edema After Hand and Wrist Surgery
NCT05440240PHASE4RECRUITINGPercutaneous Needle Fasciotomy +/- Corticosteroid Injection for Dupuytren’s Contracture
NCT06806410PHASE4ACTIVE_NOT_RECRUITINGThe Efficacy of Liposomal Bupivacaine in Ultrasound Guided Supraclavicular Nerve Blocks for Hand and Wrist Surgery
NCT01776892PHASE3WITHDRAWNCollagenase and Needle Aponeurotomy: Single Modality Versus Combination Treatment for Dupuytren’s Disease
NCT04874870PHASE3COMPLETEDEffectiveness of Splinting After Collagenase Injection
NCT01184586PHASE2UNKNOWNDupuytren’s Disease and Extracorporeal Shockwave Therapy (DupuyShock-2010)
NCT03111186PHASE2COMPLETEDIbuprofen Plus Acetaminophen Versus Oxycodone Alone After Hand Surgery
NCT07227649PHASE2NOT_YET_RECRUITINGNAC-REPAIR for Post-surgical Pain
NCT01876498Not specifiedCOMPLETEDRegistry of Patient With M. Dupuytren and Validation of the Brief MHQ
NCT01923103Not specifiedCOMPLETEDNatural Disease Progress of Dupuytren Disease
NCT02983162Not specifiedCOMPLETEDIs wGRS Associated With DD Recurrence?
NCT03031080Not specifiedWITHDRAWNBOND Study: the Benefit Of Night Splinting in Dupuytrens'
NCT03155854Not specifiedRECRUITINGThe Effects of Prophylactic Limited Palmar Fasciectomy on Surgical Outcomes and Scarring
NCT03331926Not specifiedCOMPLETEDCollagenase is a Common Treatment of MCP and PIP Joint Contractures in Dupuytrens Disease
NCT03407820Not specifiedCOMPLETEDNylon Versus Chromic Gut Sutures for Minor Hand Surgery
NCT03573765Not specifiedCOMPLETEDEpidemiology and Outcomes of Upper Limb Surgery: Analysis of Routine Data
NCT03741764Not specifiedUNKNOWNTreatment of Dupuytren’s Disease With Minimal Invasive Surgery and VIVOSORB® Resorbable Implant Device
NCT03868449Not specifiedCOMPLETEDQuestion Prompt List for Common Hand Conditions
NCT03982719Not specifiedUNKNOWNComparing the Effectiveness of Two Post-fasciectomy Rehabilitation Protocols in Patients With Dupuytren’s Disease
NCT04122313Not specifiedRECRUITINGPost-contracture Release Radiation for Dupuytren’s Disease
NCT05300893Not specifiedRECRUITINGEffectiveness of Night Splinting After Percutaneous Needle Fasciotomy in Dupuytren’s Contracture
NCT06248866Not specifiedUNKNOWNEffect Of Extracorporeal Shock Wave Therapy On Ultrasonography Changes In Patients With Palmar Fibromatosis: A Randomized Controlled Trial
NCT06330545Not specifiedRECRUITINGRadiation Therapy for Dupuytren’s Contracture Following Non-Surgical Release
NCT06788847Not specifiedRECRUITINGEvaluating Ultrasound-Guided Needle Knife for Dupuytren’s Contracture
NCT07158892Not specifiedNOT_YET_RECRUITINGUnderstanding Patient Preferences When Deciding on a Voluntary Musculoskeletal Test
NCT07443371Not specifiedNOT_YET_RECRUITINGEffect of Transfer Energy Capacitive and Resistive Therapy on Palmar Fibromatosis