TOX3

TOX high mobility group box family member 3, the group of thymocyte selection associated high mobility group box family

Basic information

Region (hg38): 16:52436417-52547802

Previous symbols: [ "TNRC9" ]

Links

ENSG00000103460

∙ NCBI:27324 ∙ OMIM:611416 ∙ HGNC:11972 ∙ Uniprot:O15405 ∙ 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 TOX3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TOX3 gene is commonly pathogenic or not. These statistics are base on transcript: . 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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1 clinvar	1
missense			41 clinvar	2 clinvar	2 clinvar	45
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	41	2	3

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TOX3	protein_coding	protein_coding	ENST00000219746	7	109798

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000504	124686	0	6	124692	0.0000241

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.16	252	310	0.814	0.0000161	3781
Missense in Polyphen		74	108.56	0.68164		1366
Synonymous	0.0363	122	123	0.996	0.00000703	1109
Loss of Function	4.57	1	26.3	0.0381	0.00000114	277

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000104	0.0000935
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000359	0.0000354
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Transcriptional coactivator of the p300/CBP-mediated transcription complex. Activates transactivation through cAMP response element (CRE) sites. Protects against cell death by inducing antiapoptotic and repressing pro-apoptotic transcripts. Stimulates transcription from the estrogen-responsive or BCL-2 promoters. Required for depolarization-induced transcription activation of the C-FOS promoter in neurons. Associates with chromatin to the estrogen-responsive C3 promoter region. {ECO:0000269|PubMed:21172805}.;
Pathway: Mesodermal Commitment Pathway;Ectoderm Differentiation (Consensus)

Intolerance Scores

loftool
rvis_EVS: 0.33
rvis_percentile_EVS: 73.61

Haploinsufficiency Scores

pHI: 0.955
hipred: Y
hipred_score: 0.643
ghis: 0.452

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.262

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Tox3
Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); homeostasis/metabolism phenotype;

Gene ontology

Biological process: regulation of transcription by RNA polymerase II;apoptotic process;regulation of apoptotic process;negative regulation of neuron apoptotic process;positive regulation of transcription, DNA-templated
Cellular component: nucleus
Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;chromatin binding;protein binding;estrogen response element binding;protein homodimerization activity;phosphoprotein binding