TBATA

Summary

TBATA (thymus, brain and testes associated, HGNC:23511) is a protein-coding gene on chromosome 10q22.1, encoding Protein TBATA (Q96M53). May play a role in spermatid differentiation.

This gene encodes a protein that regulates thymic epithelial cell proliferation and thymus size. It has been identified as a ligand for the class I human leukocyte antigen (HLA-I) in thymus. Studies of the orthologous mouse protein suggest that it may also play a role in spermatid differentiation, as well as in neuronal morphogenesis and synaptic plasticity. Polymorphisms in this gene are associated with susceptibility for multiple sclerosis (MS). Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 219793 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 66 total — 1 likely-pathogenic
• MANE Select transcript: NM_001318241

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23511
Approved symbol	TBATA
Name	thymus, brain and testes associated
Location	10q22.1
Locus type	gene with protein product
Status	Approved
Aliases	FLJ32820, spatial
Ensembl gene	ENSG00000166220
Ensembl biotype	protein_coding
OMIM	612640
Entrez	219793

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 4 protein_coding, 3 protein_coding_CDS_not_defined, 2 retained_intron, 1 nonsense_mediated_decay

ENST00000299290, ENST00000394982, ENST00000456372, ENST00000685958, ENST00000688141, ENST00000688590, ENST00000689622, ENST00000692183, ENST00000692747, ENST00000693008

RefSeq mRNA: 4 — MANE Select: NM_001318241 NM_001318241, NM_001318242, NM_001318243, NM_152710

CCDS: CCDS7308, CCDS81471, CCDS91256

Canonical transcript exons

ENST00000456372 — 11 exons

Exon	Start	End
ENSE00001101150	70775189	70775270
ENSE00001101157	70781801	70782036
ENSE00001101160	70779593	70779742
ENSE00001101162	70778557	70778636
ENSE00001144294	70784647	70784773
ENSE00001144324	70783339	70783525
ENSE00001610549	70772514	70772566
ENSE00001656922	70774213	70774357
ENSE00003733092	70777153	70777338
ENSE00003918257	70771238	70771461
ENSE00003918314	70785285	70785377

Expression profiles

Bgee: expression breadth broad, 67 present calls, max score 92.63.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1916 / max 121.2862, expressed in 9 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter ID	TPM avg	Samples expressed
109858	0.1234	5
109860	0.0260	4
109857	0.0141	3
109861	0.0138	4
109862	0.0075	3
109859	0.0045	2
109856	0.0022	1

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right testis	UBERON:0004534	92.63	gold quality
thymus	UBERON:0002370	92.22	gold quality
left testis	UBERON:0004533	91.98	gold quality
testis	UBERON:0000473	88.21	gold quality
sperm	CL:0000019	79.66	gold quality
spleen	UBERON:0002106	70.02	gold quality
lower lobe of lung	UBERON:0008949	69.48	silver quality
epithelium of nasopharynx	UBERON:0001951	67.29	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	66.22	gold quality
superficial temporal artery	UBERON:0001614	65.98	gold quality
secondary oocyte	CL:0000655	63.95	gold quality
nasal cavity epithelium	UBERON:0005384	61.77	gold quality
germinal epithelium of ovary	UBERON:0001304	61.57	gold quality
biceps brachii	UBERON:0001507	61.35	gold quality
vastus lateralis	UBERON:0001379	60.67	gold quality
heart right ventricle	UBERON:0002080	60.00	gold quality
trabecular bone tissue	UBERON:0002483	59.81	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	59.52	gold quality
mucosa of paranasal sinus	UBERON:0005030	58.64	gold quality
skin of abdomen	UBERON:0001416	58.07	gold quality
mammary duct	UBERON:0001765	57.99	gold quality
Brodmann (1909) area 23	UBERON:0013554	57.70	gold quality
skin of leg	UBERON:0001511	57.10	gold quality
oocyte	CL:0000023	57.06	gold quality
middle temporal gyrus	UBERON:0002771	56.90	gold quality
zone of skin	UBERON:0000014	56.78	gold quality
parotid gland	UBERON:0001831	56.74	gold quality
Brodmann (1909) area 46	UBERON:0006483	56.74	gold quality
adult organism	UBERON:0007023	56.09	silver quality
skin of hip	UBERON:0001554	55.96	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-CURD-79	yes	478.18
E-ANND-3	no	1.63

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): EOMES, POU1F1, SOX17

miRNA regulators (miRDB)

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

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-9500	98.62	66.54	1845
HSA-MIR-6880-5P	98.08	65.59	1282
HSA-MIR-764	94.16	64.85	656

Literature-anchored findings (GeneRIF, showing 5)

• Functional analysis of the orthologous mouse protein. (PMID:17196196)
• Functional analysis of the orthologous mouse protein. (PMID:17961552)
• C10orf27 is a candidate gene for multiple sclerosis susceptibility and pathogenesis (PMID:18208870)
• Functional analysis of the orthologous mouse protein. (PMID:19918778)
• Functional analysis of the orthologous mouse protein. (PMID:20937703)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	tbata	ENSDARG00000067831
mus_musculus	Tbata	ENSMUSG00000020096
rattus_norvegicus	Tbata	ENSRNOG00000000564

Protein

Protein identifiers

Protein TBATA — Q96M53 (reviewed: Q96M53)

Alternative names: Protein SPATIAL, Stromal protein associated with thymii and lymph node homolog, Thymus, brain and testes-associated protein

All UniProt accessions (3): A0A0A0MSR7, A0A8I5KS30, Q96M53

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in spermatid differentiation. Modulates thymic stromal cell proliferation and thymus function.

Subcellular location. Cytoplasm. Cytosol.

Similarity. Belongs to the TBATA family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q96M53-1	1	yes
Q96M53-2	2

RefSeq proteins (4): NP_001305170, NP_001305171, NP_001305172, NP_689923 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR037394	TBATA-like	Family

Pfam: PF15256

UniProt features (12 total): region of interest 4, compositionally biased region 3, splice variant 2, chain 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96M53-F1	60.70	0.14

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 0 (showing top):

GO Biological Process (2): spermatogenesis (GO:0007283), cell differentiation (GO:0030154)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (3): cytosol (GO:0005829), ciliary basal body (GO:0036064), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
developmental process involved in reproduction	1
male gamete generation	1
cellular developmental process	1
binding	1
cytoplasm	1
microtubule organizing center	1
cilium	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

372 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TBATA	NCLN	Q969V3	743
TBATA	DENND3	A2RUS2	674
TBATA	PRSS16	Q9NQE7	596
TBATA	PAXBP1	Q9Y5B6	485
TBATA	NUP98	P52948	459
TBATA	PSMB11	A5LHX3	440
TBATA	SLC46A2	Q9BY10	438
TBATA	SMIM19	Q96E16	435
TBATA	TMEM50B	P56557	432
TBATA	DOP1B	Q9Y3R5	419
TBATA	FOXN1	O15353	412
TBATA	OR8B12	Q8NGG6	390
TBATA	GET1	O00258	387
TBATA	SPATA3	Q8NHX4	370
TBATA	SLAIN2	Q9P270	363

IntAct

4 interactions, top by confidence:

A	B	Type	Score
PIH1D2	TBATA	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (3): TBATA (Two-hybrid), TBATA (Cross-Linking-MS (XL-MS)), THOC2 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A1YF19, A2T767, B0K035, F1RCE7, F7BHS0, O95997, P0DPK0, P23999, P97613, Q08B36, Q08BD8, Q09HN1, Q0VA20, Q14140, Q2KHM9, Q2QD14, Q2QD15, Q2T9X8, Q2WG80, Q3SZY3, Q3UHI0, Q3V1H1, Q5R7F8, Q5RBY6, Q5RKG1, Q5XG16, Q5ZJU5, Q6A000, Q6AYH4, Q6DF94, Q7SXC6, Q8BHE0, Q8BHZ5, Q8C804, Q8N0Z3, Q8QGU6, Q8R080, Q8WWK9, Q96C57, Q96FF9

Diamond homologs: Q32KL8, Q7TSD4, Q96M53, Q53FE4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	1
Uncertain significance	56
Likely benign	7
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
375275	NM_001318241.2(TBATA):c.157C>T (p.Arg53Cys)	Likely pathogenic

SpliceAI

2175 predictions. Top by Δscore:

Variant	Effect	Δscore
10:70772563:TTGA:T	acceptor_gain	0.9900
10:70772567:C:CC	acceptor_gain	0.9900
10:70785215:T:TA	donor_gain	0.9900
10:70785216:C:A	donor_gain	0.9900
10:70772574:C:CT	acceptor_gain	0.9800
10:70784666:T:A	donor_gain	0.9800
10:70771460:CT:C	acceptor_gain	0.9700
10:70772564:TGA:T	acceptor_gain	0.9700
10:70775187:AC:A	donor_gain	0.9600
10:70775188:CC:C	donor_gain	0.9600
10:70784645:A:AC	donor_gain	0.9500
10:70784646:C:CC	donor_gain	0.9500
10:70771462:C:CC	acceptor_gain	0.9400
10:70777214:CT:C	donor_gain	0.9400
10:70782037:C:CC	acceptor_gain	0.9400
10:70783527:T:C	acceptor_gain	0.9400
10:70772358:T:C	acceptor_gain	0.9300
10:70772565:GA:G	acceptor_gain	0.9300
10:70777212:G:T	donor_gain	0.9300
10:70782038:T:A	acceptor_gain	0.9300
10:70783526:C:CC	acceptor_gain	0.9300
10:70772358:T:TC	acceptor_gain	0.9200
10:70778634:CTT:C	acceptor_gain	0.9200
10:70782212:T:A	donor_gain	0.9200
10:70778637:C:CC	acceptor_gain	0.9100
10:70780008:T:TA	acceptor_gain	0.9100
10:70785277:GGACT:G	donor_loss	0.9100
10:70785278:GACT:G	donor_loss	0.9100
10:70785279:ACT:A	donor_loss	0.9100
10:70785280:C:CA	donor_loss	0.9100

AlphaMissense

2283 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
10:70775213:A:G	W250R	0.925
10:70775213:A:T	W250R	0.925
10:70781847:G:C	F77L	0.925
10:70781847:G:T	F77L	0.925
10:70781849:A:G	F77L	0.925
10:70775209:A:G	L251P	0.903
10:70781844:G:C	F78L	0.900
10:70781844:G:T	F78L	0.900
10:70781846:A:G	F78L	0.900
10:70778631:A:G	W145R	0.898
10:70778631:A:T	W145R	0.898
10:70781871:A:C	F69L	0.897
10:70781871:A:T	F69L	0.897
10:70781873:A:G	F69L	0.897
10:70778629:C:A	W145C	0.894
10:70778629:C:G	W145C	0.894
10:70775211:C:A	W250C	0.892
10:70775211:C:G	W250C	0.892
10:70774353:T:A	K259N	0.873
10:70774353:T:G	K259N	0.873
10:70781859:A:C	S73R	0.868
10:70781859:A:T	S73R	0.868
10:70781861:T:G	S73R	0.868
10:70775248:A:G	I238T	0.866
10:70774325:C:G	A269P	0.864
10:70775260:A:G	L234P	0.862
10:70774354:T:A	K259I	0.860
10:70778618:A:G	L149S	0.857
10:70777293:A:G	Y184H	0.845
10:70774345:G:T	A262D	0.840

dbSNP variants (sampled 300 via entrez): RS1000093566 (10:70779135 C>G,T), RS1000113995 (10:70774158 C>T), RS1000243409 (10:70775001 G>C), RS1000557850 (10:70783083 C>T), RS1000949303 (10:70778376 T>C,G), RS1001017975 (10:70778131 C>G,T), RS1001023735 (10:70783883 A>C), RS1001297621 (10:70773615 A>G), RS1001344078 (10:70784199 A>C,G), RS1001514757 (10:70776915 C>A,T), RS1001646863 (10:70781781 C>G,T), RS1001729183 (10:70781582 A>T), RS1001830889 (10:70777654 C>T), RS1002383182 (10:70773207 C>A,T), RS1002453130 (10:70777557 C>A,G)

Disease associations

OMIM: gene MIM:612640 | disease phenotypes: MIM:142623

GenCC curated gene-disease

Mondo (2): Hirschsprung disease, susceptibility to, 1 (MONDO:0007723), Hirschsprung disease (MONDO:0018309)

Orphanet (1): Hirschsprung disease (Orphanet:388)

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST005024_20	Pursuit maintenance gain	6.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0008433	pursuit maintenance gain measurement

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D006627	Hirschsprung Disease	C06.198.439; C06.405.469.158.701.439; C16.131.314.439

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

10 total (human), top 10 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	affects cotreatment, decreases methylation	1
S-(1,2-dichlorovinyl)cysteine	affects cotreatment, decreases expression	1
Fulvestrant	affects cotreatment, decreases methylation	1
Air Pollutants	decreases expression, increases abundance	1
Benzo(a)pyrene	increases methylation	1
Lipopolysaccharides	decreases expression, affects cotreatment	1
Rifampin	decreases expression	1
Smoke	increases expression	1
Tretinoin	decreases expression	1
Particulate Matter	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT02343562	PHASE4	UNKNOWN	Probiotics for Prophylaxis of Postoperative Hirschsprungs Associated Enterocolitis
NCT07186647	PHASE4	COMPLETED	Laparoscopic-Assisted Transanal Pull-Through for Hirschsprung Disease in Pediatric:Short and Intermediate Outcomes of Two Different Techniques
NCT04904081	PHASE3	UNKNOWN	Feasibility of Use of Indocyanine Green in Pediatric Colorectal Surgery
NCT03660176	PHASE3	UNKNOWN	Effects of Butyrate Enemas on Postoperative Intestinal Mobility Disorders in Hirschsprung’s Disease
NCT00630838	PHASE2	COMPLETED	Probiotic Prophylaxis of Hirschprung’s Disease Associated Enterocolitis (HAEC)
NCT01985646	EARLY_PHASE1	COMPLETED	A Trial on Conservative Treatment for Infants’ Hirschsprung Disease
NCT00478712	Not specified	RECRUITING	Hirschsprung Disease Genetic Study
NCT01515501	Not specified	COMPLETED	Endoscopic Mucosal Resection for the Diagnosis of a-Ganglionosis, a Controlled Prospective Trial (EDGE Trial)
NCT01793168	Not specified	RECRUITING	Rare Disease Patient Registry & Natural History Study - Coordination of Rare Diseases at Sanford
NCT01927809	Not specified	UNKNOWN	Genetic Mosaicism in Hirschsprung’s Disease
NCT02193685	Not specified	UNKNOWN	Identification Genetic, Immunologic and Microbial Markers of Hirschsprung Associated Enterocolitis in Children With Hirschsprung Disease
NCT02216994	Not specified	UNKNOWN	A New Scoring System Improves Diagnostic Accuracy of Intestinal Dysganglionosis –a Prospective Study
NCT02296008	Not specified	COMPLETED	3D High Resolution Anorectal Manometry in Children After Surgery for Anorectal Disorders
NCT02776176	Not specified	UNKNOWN	Enhanced Recovery After Surgery In Hirschsprung Disease
NCT02857205	Not specified	COMPLETED	MICROPRUNG : Intestinal Microbiota Analysis in Patients With or Without Hirschsprung’s Associated EnteroColitis
NCT03269812	Not specified	UNKNOWN	Laparoscopic Assisted Pull-through Versus Other Surgical Procedures for Treatment of Hirschsprung Disease
NCT03666767	Not specified	COMPLETED	Management and Outcomes of Congenital Anomalies in Low-, Middle- and High-Income Countries
NCT04020939	Not specified	COMPLETED	The Role of Indocyanine Green Angiography Fluorescence on Intestinal Resections in Pediatric Surgery.
NCT04106947	Not specified	UNKNOWN	Transition of Care for Patients With Hirschsprung Disease and Anorectal Malformations
NCT04149093	Not specified	UNKNOWN	The Association Between Calretinin and the Function of Ganglion Cells in Hirschsprung Disease
NCT04150120	Not specified	COMPLETED	eHealth as an Aid for Facilitating and Supporting Self-management in Families With Long-term Childhood Illness
NCT04213976	Not specified	UNKNOWN	Ostomy in Continuity or Conventional Ileostomy: a Retrospective Multicentric Analysis
NCT04476225	Not specified	COMPLETED	Induced Pluripotent Stem Cells for Disease Research
NCT04598841	Not specified	COMPLETED	Nutrition Support for Hirschsprung Disease
NCT04622410	Not specified	RECRUITING	Registry for Hirschsprung Disease of the BELAPS
NCT04624334	Not specified	TERMINATED	Non-invasive Assessment of Colonic Motility
NCT04730128	Not specified	COMPLETED	Translation and Validation of a Disease-specific Questionnaire for Hirschsprung’s Disease in Danish Patients
NCT04837963	Not specified	COMPLETED	Does Hirschsprung Disease Increase the Risk of Febrile Urinary Tract Infection in Children
NCT04957667	Not specified	COMPLETED	Scintigraphic Defecography for Evaluation of Functional Outcome in an Adult Hirschsprung Population
NCT05038345	Not specified	TERMINATED	Hirschsprung Disease Trends in the United States: Analysis of the National Inpatient Sample
NCT05044741	Not specified	COMPLETED	Risk Factors of Perforated HSCR in Neonates
NCT05293353	Not specified	UNKNOWN	Neokare Safety and Tolerability Assessment in Neonates With GI Problems
NCT05307419	Not specified	UNKNOWN	Full Thickness vs. Rectal Suction Biopsy in the Diagnosis of Hirschsprungs Disease
NCT05450991	Not specified	RECRUITING	Long-term Qualitative and Quantitative Outcomes of Children With Hirschsprung’s Disease and Anorectal Malformations
NCT05655845	Not specified	UNKNOWN	Risk Factors for Bowel Dysfunction at Preschool and Early Childhood Age in Children With Hirschsprung Disease
NCT06072976	Not specified	RECRUITING	The Influence of Feeding Source on the Gut Microbiome and Time to Full Feeds in Neonates With Congenital Gastrointestinal Pathologies
NCT06197061	Not specified	UNKNOWN	Comparison of Robot-assisted With Laparoscopic-assisted Modified Soave Procedure for Classical Hirschsprung Disease
NCT06573723	Not specified	RECRUITING	Institutional Registry of Rare Diseases
NCT06590142	Not specified	RECRUITING	Hirschsprung’s Advances; Working Towards Autologous tIssue therapIes
NCT06592534	Not specified	NOT_YET_RECRUITING	Babies With Enterocolitis - A Study of Faecal Calprotectin in Hirschsprung Disease (The BEACH Study)