TBATA

thymus, brain and testes associated

Basic information

Region (hg38): 10:70771238-70785401

Previous symbols: [ "C10orf27" ]

Links

ENSG00000166220 ∙ NCBI:219793 ∙ OMIM:612640 ∙ HGNC:23511 ∙ Uniprot:Q96M53 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TBATA gene.

• not_specified (57 variants)
• not_provided (1 variants)
• Hirschsprung_disease,_susceptibility_to,_1 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TBATA gene is commonly pathogenic or not. These statistics are base on transcript: NM_001318241.2. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense		1	51	6		58
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	1	51	7	0

Highest pathogenic variant AF is 0.0000142495155

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TBATA	protein_coding	protein_coding	ENST00000299290	9	14163

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.75e-10	0.113	125713	0	35	125748	0.000139

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.235	191	200	0.953	0.0000118	2256
Missense in Polyphen		59	58.721	1.0048		713
Synonymous	-0.268	84	80.9	1.04	0.00000475	707
Loss of Function	0.261	15	16.1	0.930	6.85e-7	199

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000145	0.000145
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000476	0.0000462
European (Non-Finnish)	0.000106	0.0000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.000524	0.000523
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in spermatid differentiation. Modulates thymic stromal cell proliferation and thymus function. {ECO:0000250}.

Recessive Scores

• pRec: 0.0902

Intolerance Scores

• rvis_EVS: 0.36
• rvis_percentile_EVS: 74.63

Haploinsufficiency Scores

• pHI: 0.0526
• hipred: N
• hipred_score: 0.123
• ghis: 0.402

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Tbata
• Phenotype: endocrine/exocrine gland phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); hematopoietic system phenotype; immune system phenotype

Zebrafish Information Network

• Gene name: tbata
• Affected structure: intestine
• Phenotype tag: abnormal
• Phenotype quality: lacks all parts of type

Gene ontology

• Biological process: multicellular organism development;spermatogenesis;cell differentiation
• Cellular component: cytosol