Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
Entrez ID	10716
Gene name	T-box brain transcription factor 1
Gene symbol	TBR1
Synonyms (NCBI Gene)	AUTS5IDDASTBR-1TES-56
Chromosome	2
Chromosome location	2q24.2
Summary	This gene is a member of a conserved family of genes that share a common DNA-binding domain, the T-box. T-box genes encode transcription factors involved in the regulation of numerous developmental processes. In mouse, the ortholog of this gene is express

Show/Hide all (21)

SNP ID	Visualize variation	Clinical significance	Consequence
rs762713626	C>G,T	Likely-pathogenic	Synonymous variant, coding sequence variant, missense variant
rs869312704	->GGCTGCA	Likely-pathogenic, pathogenic, pathogenic-likely-pathogenic, not-provided	Frameshift variant, coding sequence variant
rs1553510171	C>-	Likely-pathogenic	Stop gained, coding sequence variant
rs1553510215	G>C	Pathogenic	Coding sequence variant, missense variant
rs1553510217	A>T	Likely-pathogenic	Coding sequence variant, missense variant
rs1553510280	GTTTTAA>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs1553510301	T>C	Likely-pathogenic	Coding sequence variant, missense variant
rs1553510303	G>A,C	Likely-pathogenic	Stop gained, coding sequence variant, missense variant
rs1553510313	C>T	Likely-pathogenic	Stop gained, coding sequence variant
rs1553510385	G>A	Likely-pathogenic	Stop gained, coding sequence variant
rs1553510472	C>T	Likely-pathogenic	Stop gained, coding sequence variant
rs1553510492	A>G	Pathogenic, likely-pathogenic	Coding sequence variant, missense variant
rs1553510677	A>G,T	Pathogenic	Stop gained, coding sequence variant, missense variant
rs1553510680	->G	Likely-pathogenic	Frameshift variant, coding sequence variant
rs1553511175	ACG>CA	Likely-pathogenic	Frameshift variant, coding sequence variant
rs1553511216	->GCCCGCAGTC	Likely-pathogenic	Frameshift variant, coding sequence variant
rs1553511224	->C	Likely-pathogenic	Frameshift variant, coding sequence variant
rs1553511226	GC>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs1559060428	G>T	Pathogenic	Coding sequence variant, missense variant
rs1574152522	A>-	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1574152672	->C	Pathogenic	Coding sequence variant, frameshift variant

Show/Hide all (46)

miRTarBase ID	miRNA	Experiments	Reference
MIRT621869	hsa-miR-181c-3p	HITS-CLIP	23824327
MIRT621868	hsa-miR-7151-5p	HITS-CLIP	23824327
MIRT621867	hsa-miR-6777-3p	HITS-CLIP	23824327
MIRT621866	hsa-miR-3162-3p	HITS-CLIP	23824327
MIRT621865	hsa-miR-6777-5p	HITS-CLIP	23824327
MIRT621864	hsa-miR-6889-5p	HITS-CLIP	23824327
MIRT621863	hsa-miR-542-5p	HITS-CLIP	23824327
MIRT737510	hsa-miR-101-3p	Western blottingMicroarrayImmunofluorescenceqRT-PCR	33955520
MIRT621869	hsa-miR-181c-3p	HITS-CLIP	23824327
MIRT621868	hsa-miR-7151-5p	HITS-CLIP	23824327
MIRT621867	hsa-miR-6777-3p	HITS-CLIP	23824327
MIRT621866	hsa-miR-3162-3p	HITS-CLIP	23824327
MIRT621865	hsa-miR-6777-5p	HITS-CLIP	23824327
MIRT621864	hsa-miR-6889-5p	HITS-CLIP	23824327
MIRT621863	hsa-miR-542-5p	HITS-CLIP	23824327
MIRT1414932	hsa-miR-141	CLIP-seq
MIRT1414933	hsa-miR-1908	CLIP-seq
MIRT1414934	hsa-miR-200a	CLIP-seq
MIRT1414935	hsa-miR-27a	CLIP-seq
MIRT1414936	hsa-miR-27b	CLIP-seq
MIRT1414937	hsa-miR-3648	CLIP-seq
MIRT1414938	hsa-miR-375	CLIP-seq
MIRT1414939	hsa-miR-3960	CLIP-seq
MIRT1414940	hsa-miR-4282	CLIP-seq
MIRT1414941	hsa-miR-4436b-5p	CLIP-seq
MIRT1414942	hsa-miR-4438	CLIP-seq
MIRT1414943	hsa-miR-513a-5p	CLIP-seq
MIRT1414944	hsa-miR-615-5p	CLIP-seq
MIRT1414945	hsa-miR-663	CLIP-seq
MIRT1414946	hsa-miR-744	CLIP-seq
MIRT1414933	hsa-miR-1908	CLIP-seq
MIRT1414937	hsa-miR-3648	CLIP-seq
MIRT1414939	hsa-miR-3960	CLIP-seq
MIRT1414944	hsa-miR-615-5p	CLIP-seq
MIRT1414945	hsa-miR-663	CLIP-seq
MIRT1414946	hsa-miR-744	CLIP-seq
MIRT1414933	hsa-miR-1908	CLIP-seq
MIRT1414937	hsa-miR-3648	CLIP-seq
MIRT1414939	hsa-miR-3960	CLIP-seq
MIRT1414945	hsa-miR-663	CLIP-seq
MIRT1414946	hsa-miR-744	CLIP-seq
MIRT1414933	hsa-miR-1908	CLIP-seq
MIRT1414937	hsa-miR-3648	CLIP-seq
MIRT1414939	hsa-miR-3960	CLIP-seq
MIRT1414945	hsa-miR-663	CLIP-seq
MIRT1414946	hsa-miR-744	CLIP-seq

Show/Hide all (35)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000785	Component	Chromatin	IBA
GO:0000978	Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA
GO:0000978	Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	IEA
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	IBA
GO:0001661	Process	Conditioned taste aversion	IEA
GO:0001708	Process	Cell fate specification	IBA
GO:0003677	Function	DNA binding	IEA
GO:0003700	Function	DNA-binding transcription factor activity	IEA
GO:0003700	Function	DNA-binding transcription factor activity	TAS	7619531
GO:0005515	Function	Protein binding	IPI	30250039, 32814053, 35140242
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IDA	25232744
GO:0005634	Component	Nucleus	IEA
GO:0006338	Process	Chromatin remodeling	IEA
GO:0006355	Process	Regulation of DNA-templated transcription	IEA
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IBA
GO:0007420	Process	Brain development	IEA
GO:0007420	Process	Brain development	TAS	7619531
GO:0010092	Process	Specification of animal organ identity	IEA
GO:0010467	Process	Gene expression	IEA
GO:0010468	Process	Regulation of gene expression	IEA
GO:0010975	Process	Regulation of neuron projection development	IBA
GO:0010975	Process	Regulation of neuron projection development	IEA
GO:0019901	Function	Protein kinase binding	IEA
GO:0021764	Process	Amygdala development	IEA
GO:0021902	Process	Commitment of neuronal cell to specific neuron type in forebrain	IBA
GO:0021902	Process	Commitment of neuronal cell to specific neuron type in forebrain	IEA
GO:0021987	Process	Cerebral cortex development	IEA
GO:0030182	Process	Neuron differentiation	IEA
GO:0030902	Process	Hindbrain development	IEA
GO:0031490	Function	Chromatin DNA binding	IEA
GO:0045892	Process	Negative regulation of DNA-templated transcription	IDA	25232744
GO:0045893	Process	Positive regulation of DNA-templated transcription	IEA
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IEA
GO:1902667	Process	Regulation of axon guidance	IEA

MIM	HGNC	e!Ensembl
604616	11590	ENSG00000136535

Q16650

Protein name

T-box brain protein 1 (T-brain-1) (TBR-1) (TES-56)

Protein function

Transcriptional repressor involved in multiple aspects of cortical development, including neuronal migration, laminar and areal identity, and axonal projection (PubMed:25232744, PubMed:30250039). As transcriptional repressor of FEZF2, it blocks

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00907	T-box	206 → 393	T-box	Domain
PF16176	T-box_assoc	418 → 680	T-box transcription factor-associated	Family

Tissue specificity

TISSUE SPECIFICITY: Brain.

Sequence

MQLEHCLSPSIMLSKKFLNVSSSYPHSGGSELVLHDHPIISTTDNLERSSPLKKITRGMT
NQSDTDNFPDSKDSPGDVQRSKLSPVLDGVSELRHSFDGSAADRYLLSQSSQPQSAATAP
SAMFPYPGQHGPAHPAFSIGSPSRYMAHHPVITNGAYNSLLSNSSPQGYPTAGYPYPQQY
GHSYQGAPFYQFSSTQPGLVPGKAQVYLCNRPLWLKFHRHQTEMIITKQGRRMFPFLSFN
ISGLDPTAHYNIFVDVILADPNHWRFQGGKWVPCGKADTNVQGNRVYMHPDSPNTGAHWM
RQEISFGKLKLTNNKGASNNNGQMVVLQSLHKYQPRLHVVEVNEDGTEDTSQPGRVQTFT
FPETQFIAVTAYQNTDITQLKIDHNPFAKGFRDNYDTIYTGCDMDRLTPSPNDSPRSQIV
PGARYAMAGSFLQDQFVSNYAKARFHPGAGAGPGPGTDRSVPHTNGLLSPQQAEDPGAPS
PQRWFVTPANNRLDFAASAYDTATDFAGNAATLLSYAAAGVKALPLQAAGCTGRPLGYYA
DPSGWGARSPPQYCGTKSGSVLPCWPNSAAAAARMAGANPYLGEEAEGLAAERSPLPPGA
AEDAKPKDLSDSSWIETPSSIKSIDSSDSGIYEQAKRRRISPADTPVSESSSPLKSEVLA
QRDCEKNCAKDISGYYGFYSHS

Sequence length

682

Interactions

View interactions

168

Show/Hide Causal Diseases (22)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Abnormal brainstem MRI signal intensity	Likely pathogenic; Pathogenic	rs869312704	RCV001200907
Aggressive behavior	Likely pathogenic	rs1553510182, rs1684181938, rs1684275626	RCV001200911 RCV001200913 RCV001200916
Aplasia/Hypoplasia of the corpus callosum	Likely pathogenic; Pathogenic	rs1553510492	RCV000761565
Attention deficit hyperactivity disorder	Likely pathogenic	rs1553510182, rs1684167000	RCV001200911 RCV001200912
Atypical behavior	Likely pathogenic; Pathogenic	rs1553510492	RCV000761565
Autistic behavior	Likely pathogenic; Pathogenic	rs869312704, rs1553510171, rs1553510217, rs1553510280, rs1553510301, rs1553510313, rs1553510385, rs762713626, rs1553510680, rs1553511175, rs1553511216, rs1553511226, rs1553510182, rs1684167000, rs1684181938	RCV000627109 RCV000627098 RCV000627099 RCV000627100 RCV000627101 RCV000627103 RCV000627104 RCV000627106 RCV000627107 RCV000627108 RCV000627112 RCV000627114 RCV001200911 RCV001200912 RCV001200913
Delayed fine motor development	Likely pathogenic; Pathogenic	rs869312704, rs1684167000, rs1684275626	RCV001200907 RCV001200912 RCV001200916
Focal cortical dysplasia	Likely pathogenic; Pathogenic	rs869312704	RCV001200915
Gait ataxia	Likely pathogenic; Pathogenic	rs869312704	RCV001200914
Gait disturbance	Likely pathogenic	rs1684275626	RCV001200916
Hypoplasia of the frontal lobes	Likely pathogenic; Pathogenic	rs869312704	RCV001200914
Intellectual developmental disorder with autism and speech delay	Likely pathogenic; Pathogenic	rs2105280472, rs2105280445, rs2105279320, rs2105278194, rs2468098872, rs2468098938, rs2468093926, rs869312704, rs1553510679, rs2468099183, rs2468090604, rs2468090992, rs1231294235, rs2468090210, rs2468098890 View all (9 more)	RCV004789557 RCV001788531 RCV001754566 RCV006261770 RCV002291185 RCV002468806 RCV002571628 RCV000735645 RCV003120249 RCV003131707 RCV003315177 RCV003484544 RCV003989441 RCV004577968 RCV004595050 RCV005870707 RCV000735639 RCV000735640 RCV000735641 RCV000735642 RCV000735643 RCV000735644 RCV000986841 RCV000995661
Intellectual developmental disorder with speech delay, autism, and dysmorphic facies	Likely pathogenic; Pathogenic	rs869312704	RCV002515568
Intellectual disability	Likely pathogenic; Pathogenic	rs869312704, rs1553510280, rs1553511175, rs1553511226	RCV000509230 RCV001260801 RCV001260821 RCV001260826
Limb myoclonus	Likely pathogenic	rs1684181938	RCV001200913
Marfanoid habitus and intellectual disability	Likely pathogenic	rs1553510385	RCV000850483
Moderate global developmental delay	Likely pathogenic; Pathogenic	rs869312704, rs1553510171, rs1553510280, rs1553510303, rs1553510313, rs1553510385, rs1553510492, rs762713626, rs1553510680, rs1553511175, rs1553510182, rs1684167000	RCV000627110 RCV000627098 RCV000627100 RCV000627102 RCV000627103 RCV000627104 RCV000627105 RCV000627106 RCV000627107 RCV000627108 RCV001200911 RCV001200912
Neurodevelopmental disorder	Likely pathogenic; Pathogenic	rs2105280472, rs2105278359, rs869312704	RCV001374949 RCV002272824 RCV000505228
See cases	Pathogenic; Likely pathogenic	rs2105278194, rs2468098918	RCV002275252 RCV003156198
Seizure	Likely pathogenic; Pathogenic	rs869312704, rs1553510492, rs1684275626	RCV001200915 RCV000761565 RCV001200916
Severe global developmental delay	Likely pathogenic; Pathogenic	rs869312704, rs1553510217, rs1553510301, rs1553511216, rs1553511224, rs1553511226, rs1684181938, rs1684275626	RCV000627109 RCV000627099 RCV000627101 RCV000627112 RCV000627113 RCV000627114 RCV001200913 RCV001200916
TBR1-related disorder	Likely pathogenic	rs2468091740, rs2468093706	RCV003397683 RCV003410523

Show/Hide Unknown Diseases (1)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
History of neurodevelopmental disorder	Benign	rs890076	RCV000715224

Show/Hide Text Mining Associations (21)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Alcohol Related Disorders	Associate	28158988, 33948885
Antisocial Personality Disorder	Associate	28158988
Apraxias	Associate	25232744
Autism Spectrum Disorder	Associate	23160955, 30250039, 32144139, 32948248, 33948885
Autistic Disorder	Associate	25232744, 32948248, 40004448
Carcinoma Renal Cell	Associate	32070431
Congenital Abnormalities	Associate	33948885
Developmental Disabilities	Associate	30250039
Epilepsy Temporal Lobe	Associate	20411268
Frontotemporal Dementia	Associate	25556567
Glioblastoma	Associate	15494095
Heredodegenerative Disorders Nervous System	Associate	32144139
Intellectual Disability	Associate	23444363, 32948248, 34794744, 35837997
Language Disorders	Associate	25232744, 32948248
Medulloblastoma	Associate	22832583
Megalencephaly	Associate	23160955
Mental Disorders	Associate	28158988
Microcephaly	Associate	23160955
Multiple Sclerosis	Associate	36744877
Multiple Sclerosis Chronic Progressive	Stimulate	36744877
Neoplasms	Associate	22832583, 32070431

TBR1 (T-box brain transcription factor 1)