TBATA

protein-coding

thymus, brain and testes associated

Gene summary

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. [provided by RefSeq, Dec 2015]

Previous symbols:

C10orf27

MANE transcript

NM_001318241.2

Inheritance

—

ClinVar variants

P:1U:58B:7

Top phenotype

Hirschsprung disease, susceptibility to, 1

gnomAD constraint

pLI —, LoF o/e 0.93

Max pathogenic AF

—

Genomic locus

chr10:70,771,238-70,785,401

External References & Databases

Ensembl (ENSG00000166220)

Transcript & Mutation Effects

hg38 • Region Span ~14.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TBATA variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 63

not providedTotal: 1

Hirschsprung disease, susceptibility to, 1Total: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001318241.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense		1 clinvar	58 clinvar	6 clinvar		65
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	1	58	7	0	66

Highest pathogenic variant AF is 0.0000142495155

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 34 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001318241.2	RefSeq	NP_001305170.1	9	MANE Select
ENST00000456372.4	Ensembl	ENSP00000400224.3	9	MANE Select
NM_001318242.2	RefSeq	NP_001305171.1	9	Standard
NM_001318243.2	RefSeq	NP_001305172.1	9	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
tbata	Danio rerio	Structure: intestine Quality: lacks all parts of type abnormal

Gene / Model

Organism

Observed Phenotype

tbata

Danio rerio

Structure: intestine

Quality: lacks all parts of type

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

multicellular organism development
spermatogenesis
cell differentiation

Cellular Component

cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000299290
Coding exons: 9
Length: 14163
Individuals with no LoFs: 125713
Homozygous LoFs: 0
Heterozygous LoFs: 35
Defined: 125748
p: 0.000139

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.235	191	200	0.953	0.0000118	2256
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00014	0.00014	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0.000048	0.000046	rare
European (Non-Finnish)	0.00011	0.000088	rare
South Asian	0.00052	0.00052	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N

Gene Damage Prediction

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