HMGXB3

gene
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Also known as SMFKIAA0194

Summary

HMGXB3 (HMG-box containing 3, HGNC:28982) is a protein-coding gene on chromosome 5q32, encoding HMG domain-containing protein 3 (Q12766).

This gene is one of the non-canonical high mobility group (HMG) genes. The encoded protein contains an HMG-box domain found in DNA binding proteins such as transcription factors and chromosomal proteins.

Source: NCBI Gene 22993 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): Tourette syndrome (Limited, GenCC)
  • GWAS associations: 2
  • Clinical variants (ClinVar): 207 total
  • MANE Select transcript: NM_014983

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:28982
Approved symbolHMGXB3
NameHMG-box containing 3
Location5q32
Locus typegene with protein product
StatusApproved
AliasesSMF, KIAA0194
Ensembl geneENSG00000113716
Ensembl biotypeprotein_coding
OMIM619800
Entrez22993

Gene structure

Transcript identifiers

Ensembl transcripts: 19 — 16 protein_coding, 2 retained_intron, 1 nonsense_mediated_decay

ENST00000502717, ENST00000503427, ENST00000510472, ENST00000513318, ENST00000514469, ENST00000613459, ENST00000880044, ENST00000880045, ENST00000880046, ENST00000880047, ENST00000880048, ENST00000933326, ENST00000971014, ENST00000971015, ENST00000971016, ENST00000971017, ENST00000971018, ENST00000971019, ENST00000971020

RefSeq mRNA: 2 — MANE Select: NM_014983 NM_001366501, NM_014983

CCDS: CCDS54935

Canonical transcript exons

ENST00000502717 — 20 exons

ExonStartEnd
ENSE00000767100150037400150037527
ENSE00000767101150036636150036937
ENSE00000767103150030741150030839
ENSE00000767104150027020150027117
ENSE00000767105150026706150026881
ENSE00000767106150024262150024680
ENSE00000767107150018566150018697
ENSE00000767108150012255150012353
ENSE00000767109150010111150010608
ENSE00000767110150006473150006647
ENSE00001023069150050252150050461
ENSE00002046422150000739150001179
ENSE00002235087150004851150004989
ENSE00003490184150040748150040879
ENSE00003499114150048569150048685
ENSE00003504662150032454150032603
ENSE00003540711150047624150047757
ENSE00003634785150041785150041969
ENSE00003666956150045466150045685
ENSE00003847800150051725150053128

Expression profiles

Bgee: expression breadth ubiquitous, 283 present calls, max score 97.25.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 30.8939 / max 220.2426, expressed in 1821 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
5940830.89391821

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
olfactory bulbUBERON:000226497.25silver quality
type B pancreatic cellCL:000016995.51silver quality
stromal cell of endometriumCL:000225595.08gold quality
right uterine tubeUBERON:000130293.06gold quality
vena cavaUBERON:000408791.66gold quality
parotid glandUBERON:000183191.04gold quality
cardia of stomachUBERON:000116290.95gold quality
nasal cavity epitheliumUBERON:000538490.94gold quality
lateral nuclear group of thalamusUBERON:000273690.79gold quality
diaphragmUBERON:000110390.74gold quality
pylorusUBERON:000116690.29gold quality
tracheaUBERON:000312690.12gold quality
tibial nerveUBERON:000132390.04gold quality
tongue squamous epitheliumUBERON:000691990.03gold quality
subthalamic nucleusUBERON:000190689.90gold quality
body of tongueUBERON:001187689.82gold quality
dorsal plus ventral thalamusUBERON:000189789.79gold quality
triceps brachiiUBERON:000150989.78silver quality
right lobe of thyroid glandUBERON:000111989.64gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451189.59silver quality
inferior olivary complexUBERON:000212789.52gold quality
left lobe of thyroid glandUBERON:000112089.51gold quality
apex of heartUBERON:000209889.34gold quality
upper lobe of left lungUBERON:000895289.30gold quality
adenohypophysisUBERON:000219689.24gold quality
gluteal muscleUBERON:000200088.86silver quality
metanephros cortexUBERON:001053388.85gold quality
thyroid glandUBERON:000204688.80gold quality
right ovaryUBERON:000211888.79gold quality
thymusUBERON:000237088.78gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes6.15
E-CURD-10no129.44

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

59 targeting HMGXB3, 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-9-5P100.0072.282361
HSA-MIR-12118100.0065.881270
HSA-MIR-6759-5P99.9966.54785
HSA-MIR-607799.9968.042299
HSA-MIR-6891-5P99.9866.531372
HSA-MIR-1236-3P99.9468.041695
HSA-MIR-95-5P99.8972.173973
HSA-MIR-4728-5P99.8569.394718
HSA-MIR-607999.8468.541170
HSA-MIR-6785-5P99.8268.684428
HSA-MIR-205-5P99.8170.051557
HSA-MIR-3934-3P99.7665.511351
HSA-MIR-149-3P99.7268.223963
HSA-MIR-430699.7270.503630
HSA-MIR-6801-5P99.7266.50981
HSA-MIR-6883-5P99.6968.053785
HSA-MIR-6887-3P99.6667.831778
HSA-MIR-368599.6268.831621
HSA-MIR-1260A99.6166.671098
HSA-MIR-1260B99.6166.671098
HSA-MIR-1249-5P99.6166.552049
HSA-MIR-6797-5P99.6166.552084
HSA-MIR-671-5P99.5267.111277
HSA-MIR-444199.4966.563216
HSA-MIR-5584-5P99.4968.222814
HSA-MIR-127599.4767.902749
HSA-MIR-135A-5P99.3671.851601
HSA-MIR-135B-5P99.3671.631613
HSA-MIR-6828-5P99.3169.211433
HSA-MIR-488-5P99.2868.12821

Literature-anchored findings (GeneRIF, showing 2)

  • Regulation of closely juxtaposed proto-oncogene c-fms and HMGXB3 gene expression by mRNA 3’ end polymorphism in breast cancer cells. (PMID:34155128)
  • Circular RNA EGLN3 silencing represses renal cell carcinoma progression through the miR-1224-3p/HMGXB3 axis. (PMID:34274607)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriohmgxb3ENSDARG00000077823
mus_musculusHmgxb3ENSMUSG00000024622
rattus_norvegicusHmgxb3ENSRNOG00000018132

Protein

Protein identifiers

HMG domain-containing protein 3Q12766 (reviewed: Q12766)

Alternative names: HMG box-containing protein 3, Protein SMF

All UniProt accessions (4): Q12766, A0A8C8PVR7, E9PEK0, H0YAC2

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Nucleus.

RefSeq proteins (2): NP_001353430, NP_055798* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR009071HMG_box_domDomain
IPR036910HMG_box_dom_sfHomologous_superfamily
IPR039598HMGXB3Family
IPR040648HMGXB3_CxC4Domain

Pfam: PF09011, PF18717

UniProt features (9 total): region of interest 3, compositionally biased region 3, chain 1, DNA-binding region 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q12766-F164.210.32

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 99 (showing top): GCM_MYCL1, ONKEN_UVEAL_MELANOMA_UP, MORF_PML, MORF_IKBKG, ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, chr5q32, MORF_RBM8A, MORF_DDX11, GCM_BNIP1, GSE13522_CTRL_VS_T_CRUZI_Y_STRAIN_INF_SKIN_IFNG_KO_DN, CREB3L4_TARGET_GENES, DIDO1_TARGET_GENES, E2F2_TARGET_GENES, GLI4_TARGET_GENES, HES4_TARGET_GENES

GO Biological Process (1): biological_process (GO:0008150)

GO Molecular Function (1): DNA binding (GO:0003677)

GO Cellular Component (2): nucleus (GO:0005634), cellular_component (GO:0005575)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
nucleic acid binding1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

414 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
HMGXB3SNRPEP08578616
HMGXB3SLC26A2P50443589
HMGXB3SNRPD3P43331513
HMGXB3NRSN2Q9GZP1478
HMGXB3NADK2Q4G0N4461
HMGXB3TIGD6Q17RP2413
HMGXB3DHX35Q9H5Z1403
HMGXB3APOL3O95236370
HMGXB3YJU2BP13994348
HMGXB3PWWP2AQ96N64345
HMGXB3SASS6Q6UVJ0343
HMGXB3SETMARQ53H47339
HMGXB3SLC71A1Q96MC6330
HMGXB3TIGD4Q8IY51325
HMGXB3SLC30A9Q6PML9323
HMGXB3SNRPD2P43330323

IntAct

9 interactions, top by confidence:

ABTypeScore
HMGXB3ANXA7psi-mi:“MI:0915”(physical association)0.370
CDK4HMGXB3psi-mi:“MI:0915”(physical association)0.370
HMGXB3CDKN1Apsi-mi:“MI:0915”(physical association)0.370
HMGXB3PFDN1psi-mi:“MI:0915”(physical association)0.370
HMGXB3SMN1psi-mi:“MI:0915”(physical association)0.370
HMGXB3TK1psi-mi:“MI:0915”(physical association)0.370
APBB1SSPOPpsi-mi:“MI:0914”(association)0.350
DISC1HMGXB3psi-mi:“MI:0915”(physical association)0.000

BioGRID (9): HMGXB3 (Affinity Capture-RNA), HMGXB3 (Affinity Capture-RNA), HMGXB3 (Proximity Label-MS), HMGXB3 (Two-hybrid), HMGXB3 (Two-hybrid), HMGXB3 (Two-hybrid), HMGXB3 (Two-hybrid), HMGXB3 (Two-hybrid), HMGXB3 (Two-hybrid)

ESM2 similar proteins: A0A0R4IYX6, A0A1D5NVS8, A0A1L8H0H2, A0AVK6, A5GFT6, A7XYH5, A7XYJ6, B7ZS37, B8A5Y1, D4A666, E1B7L7, E1BKK0, E1BLP6, F1LMN3, F6YVB9, F8VPJ6, Q12766, Q13029, Q14B70, Q2HNT1, Q2HNT2, Q2KHR2, Q4V9H5, Q58FA4, Q5DTH5, Q5ZIE8, Q5ZIX8, Q5ZJ69, Q5ZM88, Q63679, Q63755, Q68FE9, Q69ZF8, Q6DRC5, Q6P4F7, Q6PCM1, Q6ZSZ6, Q76L83, Q80Y19, Q8BHZ4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance173
Likely benign10
Benign4

Top pathogenic / likely-pathogenic (0)

SpliceAI

3483 predictions. Top by Δscore:

VariantEffectΔscore
5:150004849:A:AGacceptor_gain1.0000
5:150004850:G:GAacceptor_gain1.0000
5:150004850:GCC:Gacceptor_gain1.0000
5:150004850:GCCAT:Gacceptor_gain1.0000
5:150006468:CTCA:Cacceptor_loss1.0000
5:150006469:TCAG:Tacceptor_loss1.0000
5:150006470:CAGGT:Cacceptor_loss1.0000
5:150006472:G:GCacceptor_loss1.0000
5:150006633:G:GTdonor_gain1.0000
5:150006634:A:Tdonor_gain1.0000
5:150006643:ATCCT:Adonor_gain1.0000
5:150006644:TCCT:Tdonor_gain1.0000
5:150006645:CCT:Cdonor_gain1.0000
5:150006646:CT:Cdonor_gain1.0000
5:150006647:TGTA:Tdonor_loss1.0000
5:150006648:G:GGdonor_gain1.0000
5:150006648:GT:Gdonor_loss1.0000
5:150006649:TAA:Tdonor_loss1.0000
5:150006652:G:GGdonor_gain1.0000
5:150012358:GTACT:Gdonor_gain1.0000
5:150012515:GGAT:Gdonor_gain1.0000
5:150018125:G:GTdonor_gain1.0000
5:150018126:A:Tdonor_gain1.0000
5:150024258:CTAG:Cacceptor_loss1.0000
5:150032604:G:GGdonor_gain1.0000
5:150037379:T:Aacceptor_gain1.0000
5:150041783:A:AGacceptor_gain1.0000
5:150041784:G:Aacceptor_loss1.0000
5:150041784:G:GAacceptor_gain1.0000
5:150041784:GA:Gacceptor_gain1.0000

AlphaMissense

8407 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
5:150006484:T:CL296P1.000
5:150006489:T:GY298D1.000
5:150006573:T:AW326R1.000
5:150006573:T:CW326R1.000
5:150006574:G:CW326S1.000
5:150006575:G:CW326C1.000
5:150006575:G:TW326C1.000
5:150006618:G:CA341P1.000
5:150018599:T:CC561R1.000
5:150018636:G:TR573M1.000
5:150018653:T:CC579R1.000
5:150032490:T:AC870S1.000
5:150032490:T:CC870R1.000
5:150032491:G:CC870S1.000
5:150032527:G:TR882M1.000
5:150032544:T:CC888R1.000
5:150037476:T:CC1034R1.000
5:150006478:C:AA294D0.999
5:150006480:T:GY295D0.999
5:150006487:T:CL297P0.999
5:150006492:T:GY299D0.999
5:150006554:T:AN319K0.999
5:150006554:T:GN319K0.999
5:150006562:T:AI322N0.999
5:150006562:T:CI322T0.999
5:150006562:T:GI322S0.999
5:150006564:A:CS323R0.999
5:150006566:T:AS323R0.999
5:150006566:T:GS323R0.999
5:150006583:T:CL329P0.999

dbSNP variants (sampled 300 via entrez): RS1000024091 (5:150038913 C>A,T), RS1000088398 (5:150037936 G>T), RS1000118570 (5:149999404 T>C), RS1000146898 (5:150015428 G>A), RS1000188063 (5:150000665 G>A), RS1000192037 (5:150043091 A>T), RS1000224117 (5:150025094 G>C), RS1000263128 (5:150030680 A>G), RS1000292105 (5:150049810 G>C), RS1000381112 (5:150044491 T>C), RS1000536110 (5:150012283 C>G), RS1000577757 (5:150041683 A>G), RS1000625537 (5:150048692 AAAT>A), RS1000661424 (5:150003440 C>G,T), RS1000679417 (5:150000241 G>A)

Disease associations

OMIM: gene MIM:619800 | disease phenotypes:

GenCC curated gene-disease

DiseaseClassificationInheritance
Tourette syndromeLimitedUnknown

Mondo (1): Tourette syndrome (MONDO:0007661)

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

StudyTraitp-value
GCST010397_24Gut microbiota (bacterial taxa, rank normal transformation method)1.000000e-06
GCST90002394_27Monocyte percentage of white cells7.000000e-16

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0007874gut microbiome measurement
EFO:0007989monocyte percentage of leukocytes

MeSH disease descriptors (1)

DescriptorNameTree numbers
D005879Tourette SyndromeC10.228.140.079.898; C10.228.662.825.800; C10.574.500.850; C16.320.400.820; F03.625.992.850

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

22 total (human), top 22 by PubMed support.

ChemicalActions (top 5)PubMed papers
aristolochic acid Iincreases expression1
GSK-J4increases expression1
TAK-243increases sumoylation1
pirinixic acidincreases activity, increases expression, affects binding1
bisphenol Aaffects cotreatment, increases methylation, decreases methylation1
geraniolincreases expression1
sodium arseniteincreases expression1
manganese chloridedecreases expression, increases abundance1
abrineincreases expression1
eprenetapoptaffects expression1
Fulvestrantaffects cotreatment, increases methylation1
Arsenicaffects methylation1
Asbestosaffects expression1
Benzo(a)pyrenedecreases methylation1
Doxorubicindecreases expression1
Manganesedecreases expression, increases abundance1
Seleniumincreases expression1
Smokedecreases expression1
Dihydrotestosteroneincreases expression1
Thiramincreases expression1
Cadmium Chloridedecreases expression1
Okadaic Acidincreases expression1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT00152750PHASE4UNKNOWNStudy of Clonidine on Sleep Architecture in Children With Tourette’s Syndrome (TS) and Comorbid ADHD
NCT00226824PHASE4TERMINATEDSafety Study of Galantamine in Tic Disorders
NCT00241176PHASE4COMPLETEDOpen Label Trial of Aripiprazole in Children and Adolescents With Tourette’s Disorder
NCT00370838PHASE4COMPLETEDComparison of Keppra and Clonidine in the Treatment of Tics
NCT01018056PHASE4COMPLETEDDeveloping New Treatments for Tourette Syndrome: Therapeutic Trials With Modulators of Glutamatergic Neurotransmission
NCT01547000PHASE4COMPLETEDGuanfacine in Children With Tic Disorders
NCT03239210PHASE4COMPLETEDEffects of Ondansetron in Obsessive-compulsive and Tic Disorders
NCT00004376PHASE3COMPLETEDPhase III Randomized, Double-Blind, Placebo-Controlled Study of Guanfacine for Tourette Syndrome and Attention Deficit Hyperactivity Disorder
NCT00206323PHASE3COMPLETEDA Randomized, Placebo-controlled, Tourette Syndrome Study.
NCT00206336PHASE3COMPLETEDAn Open-label Study to Determine the Efficacy and Safety of Topiramate in the Treatment of Tourette Syndrome.
NCT00478842PHASE3COMPLETEDPallidal Stimulation and Gilles de la Tourette Syndrome
NCT00681863PHASE3TERMINATEDOpen-label Extension Study of Pramipexole in the Treatment of Children and Adolescents With Tourette Syndrome
NCT01501695PHASE3COMPLETEDPhase III Study of 5LGr to Treat Tic Disorder
NCT03087201PHASE3COMPLETEDCANNAbinoids in the Treatment of TICS (CANNA-TICS)
NCT03487783PHASE3COMPLETEDAripiprazole Oral Solution in the Treatment of Children and Adolescents With Tourette’s Syndrome
NCT03567291PHASE3TERMINATEDEvaluation of Safety and Tolerability of Long-term TEV-50717 (Deutetrabenazine) for Treatment of Tourette Syndrome in Children and Adolescents
NCT03571256PHASE3COMPLETEDA Study to Test if TEV-50717 is Effective in Relieving Tics Associated With Tourette Syndrome (TS)
NCT06021522PHASE3ACTIVE_NOT_RECRUITINGA Study to Evaluate Long-term Safety of Ecopipam Tablets in Children, Adolescents and Adults With Tourette’s Disorder
NCT00004393PHASE2COMPLETEDPhase II Double Blind Placebo Controlled Trial of Risperidone in Tourette Syndrome
NCT00004652PHASE2COMPLETEDPhase II Pilot Controlled Study of Short Vs Longer Term Pimozide (Orap) Therapy in Tourette Syndrome
NCT00231985PHASE2COMPLETEDEffectiveness of Behavior Therapy and Psychosocial Therapy for the Treatment of Tourette Syndrome and Chronic Tic Disorder
NCT00311909PHASE2COMPLETEDThalamic Deep Brain Stimulation for Tourette Syndrome
NCT00529308PHASE2COMPLETEDTranscranial Magnetic Stimulation (TMS) for Individuals With Tourette’s Syndrome
NCT00558467PHASE2COMPLETEDPramipexole Pilot Phase II Study in Children and Adolescents With Tourette Disorder According to DSM-IV Criteria
NCT01043549PHASE2TERMINATEDRepetitive Transcranial Magnetic Stimulation of the Posterior Parietal Cortex in Patients Suffering From Gilles de la Tourette Syndrome
NCT01133353PHASE2WITHDRAWNA Study of the Effectiveness and Safety of Tetrabenazine MR in Pediatric Subjects With Tourette’s Syndrome
NCT01475383PHASE2WITHDRAWNStudy Evaluating The Safety And Efficacy Of PF-03654746 In Adult Subjects With Tourette’s Syndrome
NCT01647269PHASE2COMPLETEDA Trial of Bilateral Deep Brain Stimulation to the Globus Pallidus Internum in Tourette Syndrome
NCT01904773PHASE2COMPLETEDSafety, Tolerability, Pharmacokinetic, and Efficacy Study of AZD5213 in Adolescents With Tourette’s Disorder
NCT02102698PHASE2COMPLETEDEcopipam Treatment of Tourette’s Syndrome in Subjects 7-17 Years
NCT02217007PHASE2WITHDRAWNA Trial Evaluating the Efficacy, Safety, and Pharmacokinetics of SNC-102 in Subjects With Tourette Syndrome
NCT02247206PHASE2COMPLETEDVoIP Delivered Behavior Therapy for Tourette Syndrome
NCT02581865PHASE2COMPLETEDSafety and Efficacy Study of NBI-98854 in Adults With Tourette Syndrome
NCT02619084PHASE2COMPLETEDSubthalamic Stimulation in Tourette’s Syndrome
NCT02679079PHASE2COMPLETEDSafety and Efficacy Study of NBI-98854 in Children and Adolescents With Tourette Syndrome
NCT02879578PHASE2COMPLETEDSafety and Tolerability Study of NBI-98854 for the Treatment of Subjects With Tourette Syndrome
NCT03066193PHASE2COMPLETEDEfficacy of a Therapeutic Combination of Dronabinol and PEA for Tourette Syndrome
NCT03247244PHASE2TERMINATEDSafety and Efficacy of Cannabis in Tourette Syndrome
NCT03325010PHASE2COMPLETEDSafety, Tolerability, and Efficacy of NBI-98854 for the Treatment of Pediatric Subjects With Tourette Syndrome
NCT03444038PHASE2COMPLETEDOpen-Label Safety and Tolerability Study of NBI-98854 for the Treatment of Pediatric Subjects With Tourette Syndrome
  • Associated diseases: Tourette syndrome
  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): Tourette syndrome