TOX3

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

Basic information

Region (hg38): 16:52436416-52547802

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.

• Inborn genetic diseases (22 variants)
• not provided (3 variants)

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.

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	1
missense			21	1	2	24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	1	3

Variants in TOX3

This is a list of pathogenic ClinVar variants found in the TOX3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
16-52439246-T-A		not specified	Uncertain significance (Dec 07, 2021)
16-52439280-G-A		not specified	Uncertain significance (Mar 28, 2023)
16-52439298-G-A		not specified	Uncertain significance (Jan 23, 2024)
16-52439332-A-T		not specified	Uncertain significance (May 23, 2023)
16-52439334-G-C		not specified	Uncertain significance (Mar 13, 2023)
16-52439418-C-T		not specified	Likely benign (Jan 29, 2024)
16-52439419-G-A			Benign (Jul 17, 2018)
16-52439430-T-A		not specified	Uncertain significance (Jun 07, 2023)
16-52439433-T-A		not specified	Uncertain significance (Jun 07, 2023)
16-52439504-G-T		not specified	Uncertain significance (Jan 17, 2023)
16-52439588-C-G		not specified	Uncertain significance (Nov 14, 2023)
16-52439670-G-A		not specified	Uncertain significance (Feb 11, 2022)
16-52439718-G-T		not specified	Uncertain significance (Jan 19, 2024)
16-52439730-G-A		not specified	Uncertain significance (Jun 28, 2023)
16-52439739-T-C		not specified	Uncertain significance (Mar 20, 2023)
16-52439743-C-T		not specified	Uncertain significance (Aug 22, 2022)
16-52439771-G-T		not specified	Uncertain significance (Mar 05, 2024)
16-52439807-G-A			Benign (Dec 31, 2019)
16-52439898-G-A		not specified	Uncertain significance (Sep 29, 2022)
16-52444344-T-C		not specified	Uncertain significance (Dec 21, 2022)
16-52446064-T-A		not specified	Uncertain significance (Apr 13, 2023)
16-52446203-C-G		not specified	Uncertain significance (Nov 29, 2021)
16-52450405-C-T			Benign (May 24, 2018)
16-52450461-C-T		not specified	Uncertain significance (Mar 12, 2024)
16-52450491-C-T		not specified	Uncertain significance (Dec 03, 2021)

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

• 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