MBLAC1

gene
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Also known as MGC49416

Summary

MBLAC1 (metallo-beta-lactamase domain containing 1, HGNC:22180) is a protein-coding gene on chromosome 7q22.1, encoding Metallo-beta-lactamase domain-containing protein 1 (A4D2B0). Endoribonuclease that catalyzes the hydrolysis of histone-coding pre-mRNA 3’-end.

Enables RNA endonuclease activity and metal ion binding activity. Involved in histone mRNA metabolic process; mRNA 3’-end processing; and positive regulation of G1/S transition of mitotic cell cycle. Located in cytoplasm and nucleus.

Source: NCBI Gene 255374 — RefSeq curated summary.

At a glance

  • GWAS associations: 7
  • Clinical variants (ClinVar): 13 total — 1 likely-pathogenic
  • MANE Select transcript: NM_203397

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:22180
Approved symbolMBLAC1
Namemetallo-beta-lactamase domain containing 1
Location7q22.1
Locus typegene with protein product
StatusApproved
AliasesMGC49416
Ensembl geneENSG00000214309
Ensembl biotypeprotein_coding
OMIM620906
Entrez255374

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000398075, ENST00000421390, ENST00000905248

RefSeq mRNA: 1 — MANE Select: NM_203397 NM_203397

CCDS: CCDS43620

Canonical transcript exons

ENST00000398075 — 2 exons

ExonStartEnd
ENSE00001531468100127368100128495
ENSE00001531469100126967100127064

Expression profiles

Bgee: expression breadth ubiquitous, 173 present calls, max score 86.80.

FANTOM5 (CAGE): breadth broad, TPM avg 0.7196 / max 27.0525, expressed in 435 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
799300.7196435

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047386.80gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099180.41silver quality
prefrontal cortexUBERON:000045176.96gold quality
tendon of biceps brachiiUBERON:000818876.65silver quality
Brodmann (1909) area 9UBERON:001354075.98gold quality
right hemisphere of cerebellumUBERON:001489075.93gold quality
right frontal lobeUBERON:000281075.63gold quality
cerebellar hemisphereUBERON:000224575.28gold quality
anterior cingulate cortexUBERON:000983575.21gold quality
cerebellar cortexUBERON:000212975.16gold quality
dorsolateral prefrontal cortexUBERON:000983474.88gold quality
cerebellumUBERON:000203774.61gold quality
frontal cortexUBERON:000187074.32gold quality
endothelial cellCL:000011574.26silver quality
neocortexUBERON:000195074.10gold quality
apex of heartUBERON:000209873.85gold quality
cerebral cortexUBERON:000095672.73gold quality
mucosa of transverse colonUBERON:000499172.26gold quality
lower esophagus muscularis layerUBERON:003583371.85gold quality
lower esophagusUBERON:001347371.80gold quality
nucleus accumbensUBERON:000188271.42gold quality
cortical plateUBERON:000534371.41gold quality
brainUBERON:000095571.27gold quality
forebrainUBERON:000189071.26gold quality
right ovaryUBERON:000211871.08gold quality
right atrium auricular regionUBERON:000663171.08gold quality
esophagogastric junction muscularis propriaUBERON:003584171.05gold quality
amygdalaUBERON:000187671.01gold quality
cardiac atriumUBERON:000208170.96gold quality
putamenUBERON:000187470.93gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3no0.88

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

18 targeting MBLAC1, 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-34A-5P99.9971.211784
HSA-MIR-449A99.9971.051776
HSA-MIR-34C-5P99.9770.451577
HSA-MIR-449B-5P99.9770.261580
HSA-MIR-449299.8768.253611
HSA-MIR-4713-5P99.7867.801794
HSA-MIR-431999.7669.832586
HSA-MIR-2116-3P99.7464.32889
HSA-MIR-548AU-3P99.7068.221373
HSA-MIR-670-5P99.6769.941565
HSA-MIR-320299.6667.702737
HSA-MIR-6887-3P99.6667.831778
HSA-MIR-444199.4966.563216
HSA-MIR-125A-5P99.3670.591640
HSA-MIR-125B-5P99.3670.361662
HSA-MIR-5008-5P98.4265.871019
HSA-MIR-4732-3P97.1565.45881
HSA-MIR-345-5P96.4066.43663

Literature-anchored findings (GeneRIF, showing 1)

  • The cellular, genetic, biochemical, substrate selectivity, and crystallographic studies have been reported providing evidence that endoribonuclease, MBLAC1, is selective for 3’ processing of replication-dependent histone pre-mRNA during the S-phase of the cell cycle. (PMID:30507380)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriomblac1ENSDARG00000077314
mus_musculusMblac1ENSMUSG00000049285
rattus_norvegicusMblac1ENSRNOG00000082402
drosophila_melanogasterCG9117FBGN0031766
caenorhabditis_elegansWBGENE00018738

Protein

Protein identifiers

Metallo-beta-lactamase domain-containing protein 1A4D2B0 (reviewed: A4D2B0)

Alternative names: Endoribonuclease MBLAC1

All UniProt accessions (2): A4D2B0, C9JAV3

UniProt curated annotations — full annotation on UniProt →

Function. Endoribonuclease that catalyzes the hydrolysis of histone-coding pre-mRNA 3’-end. Involved in histone pre-mRNA processing during the S-phase of the cell cycle, which is required for entering/progressing through S-phase. Cleaves histone pre-mRNA at a major and a minor cleavage site after the 5’-ACCCA-3’ and the 5’-ACCCACA-3’ sequence, respectively, and located downstream of the stem-loop. May require the presence of the HDE element located at the histone pre-RNA 3’-end to avoid non-specific cleavage.

Subunit / interactions. Homodimer.

Subcellular location. Cytoplasm. Cytosol. Nucleus.

Cofactor. Binds 2 Zn(2+) ions per subunit.

Domain organisation. Contains four of the five characteristic MBL-fold metal-binding motifs, with two waters completing metal coordination.

Similarity. Belongs to the metallo-beta-lactamase superfamily. Glyoxalase II family.

RefSeq proteins (1): NP_981942* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001279Metallo-B-lactamasDomain
IPR036866RibonucZ/Hydroxyglut_hydroHomologous_superfamily
IPR039344MBLAC1Family

Pfam: PF00753

Catalyzed reactions (Rhea), 1 shown:

  • a ribonucleotidyl-ribonucleotide-RNA + H2O = a 3’-end ribonucleotide-RNA + a 5’-end 5’-phospho-ribonucleoside-RNA + H(+) (RHEA:68096)

UniProt features (44 total): strand 16, binding site 8, helix 7, mutagenesis site 3, turn 3, region of interest 2, sequence variant 2, sequence conflict 2, chain 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
4V0HX-RAY DIFFRACTION1.79

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-A4D2B0-F189.220.80

Functional residue map

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

Ligand- & substrate-binding residues (8): 231; 114; 116; 118; 119; 169; 192; 192

Mutagenesis-validated functional residues (3):

PositionPhenotype
169loss of endoribonuclease activity; when associated with a-192 and a-231.
192loss of endoribonuclease activity; when associated with a-169 and a-231.
231loss of endoribonuclease activity; when associated with a-169 and a-192.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 62 (showing top): GOMF_ENDONUCLEASE_ACTIVITY, GOMF_RNA_NUCLEASE_ACTIVITY, GOMF_NUCLEASE_ACTIVITY, SHEPARD_CRASH_AND_BURN_MUTANT_UP, GOBP_CELL_CYCLE_PHASE_TRANSITION, GOBP_POSITIVE_REGULATION_OF_MITOTIC_CELL_CYCLE, GOBP_POSITIVE_REGULATION_OF_G1_S_TRANSITION_OF_MITOTIC_CELL_CYCLE, GOMF_RNA_ENDONUCLEASE_ACTIVITY, GOBP_REGULATION_OF_CELL_CYCLE, GOBP_MRNA_3_END_PROCESSING, GOBP_REGULATION_OF_CELL_CYCLE_G1_S_PHASE_TRANSITION, GOBP_POSITIVE_REGULATION_OF_CELL_CYCLE_PROCESS, GOBP_CELL_CYCLE_G1_S_PHASE_TRANSITION, GOBP_MITOTIC_CELL_CYCLE, GOBP_HISTONE_MRNA_METABOLIC_PROCESS

GO Biological Process (3): histone mRNA metabolic process (GO:0008334), mRNA 3’-end processing (GO:0031124), positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)

GO Molecular Function (4): RNA endonuclease activity (GO:0004521), hydrolase activity (GO:0016787), metal ion binding (GO:0046872), protein binding (GO:0005515)

GO Cellular Component (3): nucleus (GO:0005634), cytoplasm (GO:0005737), cytosol (GO:0005829)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure2
mRNA metabolic process1
mRNA processing1
RNA 3’-end processing1
G1/S transition of mitotic cell cycle1
positive regulation of mitotic cell cycle phase transition1
positive regulation of cell cycle G1/S phase transition1
regulation of G1/S transition of mitotic cell cycle1
endonuclease activity1
RNA nuclease activity1
catalytic activity1
cation binding1
binding1
intracellular membrane-bounded organelle1
intracellular anatomical structure1
cytoplasm1

Protein interactions and networks

STRING

240 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
MBLAC1MBLAC2Q68D91664
MBLAC1LACTB2Q53H82642
MBLAC1ELAC1Q9H777531
MBLAC1HAGHLQ6PII5497
MBLAC1DCLRE1AQ6PJP8493
MBLAC1ATOSAQ32MH5489
MBLAC1HAGHQ16775479
MBLAC1ZC3H6P61129479
MBLAC1ELAC2Q9BQ52478
MBLAC1INTS9Q9NV88465
MBLAC1KBTBD4Q9NVX7456
MBLAC1WASHC4Q2M389447
MBLAC1ISG20L2Q9H9L3425
MBLAC1DCLRE1BQ9H816415
MBLAC1PNKDQ8N490399

IntAct

4 interactions, top by confidence:

ABTypeScore
MBLAC1H1-7psi-mi:“MI:0914”(association)0.560
MBLAC1H1-7psi-mi:“MI:0915”(physical association)0.560
PRNPWDR91psi-mi:“MI:0914”(association)0.350

BioGRID (16): H1FNT (Affinity Capture-MS), CLP1 (Affinity Capture-MS), MBLAC1 (Two-hybrid), MBLAC1 (Two-hybrid), MBLAC1 (Two-hybrid), MBLAC1 (Two-hybrid), MBLAC1 (Two-hybrid), MBLAC1 (Two-hybrid), MBLAC1 (Two-hybrid), MBLAC1 (Two-hybrid), MBLAC1 (Two-hybrid), MBLAC1 (Two-hybrid), C10orf55 (Two-hybrid), MBLAC1 (Affinity Capture-MS), MBLAC1 (Affinity Capture-RNA)

ESM2 similar proteins: A2XFU4, A2XFU5, A2XVN3, A2YQ58, A3AVP1, A4D2B0, A4IFA8, A7HDG9, A8ID74, A8IF44, A8J1V4, A8MPS7, B1WBV0, B4UH39, B8JE35, G8XHD8, O86507, P29784, P52824, Q08325, Q0D3F2, Q0D9V6, Q0DSH9, Q10MI9, Q1CW46, Q2HJB0, Q2IQ95, Q2RSY6, Q498J9, Q50863, Q50864, Q53JI9, Q53U11, Q566Q8, Q5GA22, Q5NAI7, Q6AYD1, Q72DW3, Q758T2, Q82JN8

Diamond homologs: A4D2B0, Q11123, Q2HJB0, Q498J9, Q6AYD1, Q8BWY4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic1
Uncertain significance12
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
3358894NM_203397.3(MBLAC1):c.-28-1G>ALikely pathogenic

SpliceAI

256 predictions. Top by Δscore:

VariantEffectΔscore
7:100127367:GCCC:Gacceptor_gain0.9900
7:100127130:GGAC:Gdonor_gain0.9800
7:100127131:G:GTdonor_gain0.9800
7:100127366:A:AGacceptor_gain0.9800
7:100127367:G:GGacceptor_gain0.9800
7:100127037:G:GGdonor_gain0.9700
7:100127104:G:GTdonor_gain0.9700
7:100127367:GC:Gacceptor_gain0.9700
7:100127134:G:GGdonor_gain0.9600
7:100127367:GCC:Gacceptor_gain0.9600
7:100127366:AGCCC:Aacceptor_gain0.9500
7:100127367:GCCCG:Gacceptor_gain0.9500
7:100127105:A:Tdonor_gain0.9400
7:100127202:G:GTdonor_gain0.9400
7:100127043:C:Tdonor_gain0.9300
7:100127093:G:Tdonor_gain0.9200
7:100126994:G:GTdonor_gain0.9100
7:100127364:CCA:Cacceptor_loss0.9100
7:100127131:GAC:Gdonor_gain0.9000
7:100127178:G:GTdonor_gain0.9000
7:100127363:CCCAG:Cacceptor_gain0.8900
7:100127364:CCAGC:Cacceptor_gain0.8900
7:100127365:CAGCC:Cacceptor_gain0.8900
7:100127129:AGGAC:Adonor_gain0.8800
7:100127130:GGACG:Gdonor_gain0.8800
7:100127046:G:GTdonor_gain0.8700
7:100127036:A:AGdonor_gain0.8600
7:100127179:G:Tdonor_gain0.8600
7:100127366:AG:Aacceptor_gain0.8600
7:100127367:G:Tacceptor_gain0.8600

AlphaMissense

1657 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
7:100127921:A:CS176R0.989
7:100127923:C:AS176R0.989
7:100127923:C:GS176R0.989
7:100127975:T:CF194L0.983
7:100127977:T:AF194L0.983
7:100127977:T:GF194L0.983
7:100127749:T:AD118E0.977
7:100127749:T:GD118E0.977
7:100127748:A:TD118V0.975
7:100127970:A:TD192V0.975
7:100128045:G:CR217P0.975
7:100127971:T:AD192E0.974
7:100127971:T:GD192E0.974
7:100128098:T:CF235L0.972
7:100128100:T:AF235L0.972
7:100128100:T:GF235L0.972
7:100127976:T:CF194S0.969
7:100128014:A:CS207R0.969
7:100128016:T:AS207R0.969
7:100128016:T:GS207R0.969
7:100128075:T:AV227D0.969
7:100128004:G:CW203C0.967
7:100128004:G:TW203C0.967
7:100127771:T:CF126L0.963
7:100127772:T:CF126S0.963
7:100127773:C:AF126L0.963
7:100127773:C:GF126L0.963
7:100127748:A:CD118A0.960
7:100127761:C:AN122K0.960
7:100127761:C:GN122K0.960

dbSNP variants (sampled 300 via entrez): RS1000392813 (7:100128116 G>T), RS1000694652 (7:100126631 A>G), RS1001735567 (7:100125562 G>A), RS1002288845 (7:100125423 T>C), RS1002674646 (7:100126929 G>A), RS1003158022 (7:100126779 T>A,C), RS1004086645 (7:100127995 G>A,T), RS1004314645 (7:100125759 G>C), RS1004751809 (7:100126015 T>C), RS1005215226 (7:100125422 C>T), RS1006252036 (7:100126458 G>C), RS1006597026 (7:100127496 T>G), RS1007039184 (7:100127699 G>A,C,T), RS1007270102 (7:100127389 C>A,T), RS1008189590 (7:100128980 T>C)

Disease associations

OMIM: gene MIM:620906 | disease phenotypes: MIM:192500

GenCC curated gene-disease

Mondo (1): familial long QT syndrome (MONDO:0019171)

Orphanet (2): Romano-Ward syndrome (Orphanet:101016), Congenital long QT syndrome (Orphanet:768)

HPO phenotypes

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

GWAS associations

7 associations (top):

StudyTraitp-value
GCST005196_147Coronary artery disease2.000000e-06
GCST009281_6Microalbuminuria in type 1 diabetes1.000000e-08
GCST010002_259Refractive error3.000000e-16
GCST010083_207Hemoglobin levels6.000000e-26
GCST010702_48Subcortical volume (MOSTest)6.000000e-10
GCST010703_289Brain morphology (MOSTest)6.000000e-15
GCST90002383_428Hematocrit2.000000e-27

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0004509hemoglobin measurement
EFO:0004346neuroimaging measurement
EFO:0004348hematocrit

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

13 total (human), top 13 by PubMed support.

ChemicalActions (top 5)PubMed papers
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
abrineincreases expression1
jinfukangincreases expression1
Glyphosatedecreases expression1
Benzo(a)pyreneaffects methylation1
Cisplatindecreases expression1
Potassium Dichromateincreases expression1
Sodium Dodecyl Sulfateincreases expression1
Tobacco Smoke Pollutionincreases expression1
Urethanedecreases expression1
Valproic Acidaffects expression1
2,4-Dichlorophenoxyacetic Aciddecreases expression1
Particulate Matterdecreases expression1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT02513940PHASE4COMPLETEDInfluence of Testosterone Administration on Drug-Induced QT Interval Prolongation and Torsades de Pointes
NCT03834883PHASE4COMPLETEDReducing the Risk of Drug-Induced QT Interval Lengthening in Women
NCT04169100PHASE4UNKNOWNNovel Form of Acquired Long QT Syndrome
NCT04675788PHASE4COMPLETEDNovel Approaches for Minimizing Drug-Induced QT Interval Lengthening
NCT01648205PHASE2COMPLETEDLong-term Efficacy Study of Sodium Channel Blocker in LQT3 Patients
NCT02412709PHASE2UNKNOWNLong QT Syndrome Screening in Newborns
NCT04581408PHASE2COMPLETEDMutation-specific Therapy for the Long QT Syndrome
NCT00316459PHASE1COMPLETEDStudy Evaluating the Effects of Multiple Oral Doses of ERB-041 on Cardiac Repolarization in Healthy Subjects
NCT01849003PHASE1COMPLETEDStudy of the Effect of GS-6615 in Subjects With LQT-3
NCT02365532PHASE1COMPLETEDEffect of Oral GS-6615 on Dofetilide-Induced QT Prolongation, Safety, and Tolerability in Healthy Adults
NCT02412098PHASE1COMPLETEDPharmacokinetics of Eleclazine in Adults With Normal and Impaired Hepatic Function
NCT02441829PHASE1COMPLETEDPharmacokinetics of Eleclazine in Adults With Normal and Impaired Renal Function
NCT05759962PHASE1COMPLETEDPhase 1 Study of LQT-1213 in Healthy Adults
NCT05906732PHASE1/PHASE2TERMINATEDStudy of LQT-1213 on QTc-induced Prolongation in Healthy Adult Subjects (Part1) and on Congenital Long QT in Patients Diagnosed With Type 2 or 3 Long QT Syndrome (Part 2).
NCT00005176Not specifiedCOMPLETEDLong QT Syndrome-Population Genetics and Cardiac Studies
NCT00005250Not specifiedCOMPLETEDLinkage Study of Long QT Syndrome In An Amish Kindred
NCT00005367Not specifiedCOMPLETEDEpidemiology of Long QTand Asian Sudden Death in Sleep
NCT00221832Not specifiedUNKNOWNMolecular Genetic Screening and Identification of Congenital Arrhythmogenic Diseases
NCT00292032Not specifiedCOMPLETEDRegistry of Unexplained Cardiac Arrest
NCT00335036Not specifiedTERMINATEDPediatric Lead Extractability and Survival Evaluation (PLEASE)
NCT00399412Not specifiedCOMPLETEDECG Signal Collection From Long QT Syndrome, Wide QRS Complexes, Heart Failure, and Cardiac Resynchronization Patients
NCT00488254Not specifiedCOMPLETEDThe Long QT Syndrome in Pregnancy
NCT00588965Not specifiedCOMPLETEDEffect of Beta-blocker Therapy on QTc Response in Exercise and Recovery in Normal Subjects
NCT01705925Not specifiedCOMPLETEDMulticenter Evaluation of Children and Young Adults With Genotype Positive Long QT Syndrome
NCT01903564Not specifiedCOMPLETEDFetal and Neonatal Magnetophysiology
NCT02082431Not specifiedCOMPLETEDDetermine the Incidence of Long QT Amongst a Large Cohort of Subjects Diagnosed With Unilateral or Bilateral Sensorineural Hearing Loss.
NCT02413450Not specifiedENROLLING_BY_INVITATIONDerivation of Human Induced Pluripotent Stem (iPS) Cells to Heritable Cardiac Arrhythmias
NCT02425189Not specifiedCOMPLETEDThe Canadian National Long QT Syndrome Registry
NCT02439645Not specifiedTERMINATEDA Registry to Determine the Clinical and Genetic Risk Factors for Torsade De Pointes
NCT02439658Not specifiedUNKNOWNGenetics of QT Prolongation With Antiarrhythmics
NCT02549664Not specifiedCOMPLETEDExercise in Genetic Cardiovascular Conditions
NCT02581241Not specifiedCOMPLETEDAbnormal QT-Response to the Sudden Tachycardia Provoked by Standing in Individuals With Drug-induced Long QT Syndrome
NCT02680080Not specifiedCOMPLETEDEffect of Grapefruit on QT Interval in Healthy Volunteers and Patients With Congenital Long QT Syndrome
NCT02775513Not specifiedUNKNOWNMetabolism of Patients With Genetically Caused Cardiac Arrhythmia
NCT02814981Not specifiedUNKNOWNHydroxyzine and Risk of Prolongation of QT Interval
NCT02876380Not specifiedCOMPLETEDProspective Identification of Long QT Syndrome in Fetal Life
NCT03182777Not specifiedCOMPLETEDSafety of Local Dental Anesthesia in Patients With Cardiac Channelopathies
NCT03544918Not specifiedCOMPLETEDPrevalence of Congenital Long QT Syndrome and Acquired QT Prolongation in a Hospital Cohort
NCT03642405Not specifiedUNKNOWNDrug-induced Repolarization ECG Changes
NCT03678311Not specifiedCOMPLETEDLong QT Syndrome and Sleep Apnea
  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): familial long QT syndrome