TOX

thymocyte selection associated high mobility group box, the group of thymocyte selection associated high mobility group box family

Basic information

Region (hg38): 8:58805411-59119147

Links

ENSG00000198846 ∙ NCBI:9760 ∙ OMIM:606863 ∙ HGNC:18988 ∙ Uniprot:O94900 ∙ 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 TOX gene.

• Inborn genetic diseases (13 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TOX 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			13			13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	13	1	0

Variants in TOX

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

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

Position	Type	Phenotype	Significance	ClinVar
8-58807775-T-C		not specified	Uncertain significance (Aug 23, 2021)
8-58808157-G-C		not specified	Uncertain significance (Jan 03, 2024)
8-58808157-G-T		not specified	Uncertain significance (Dec 21, 2021)
8-58808160-G-A		not specified	Uncertain significance (Dec 18, 2023)
8-58808202-G-C		not specified	Uncertain significance (Jan 23, 2024)
8-58815441-T-A		not specified	Uncertain significance (Aug 17, 2022)
8-58815446-G-T		not specified	Uncertain significance (Sep 06, 2022)
8-58815523-G-T		not specified	Uncertain significance (Nov 09, 2021)
8-58815531-G-A		not specified	Uncertain significance (Feb 27, 2023)
8-58815564-T-C		not specified	Uncertain significance (Mar 11, 2024)
8-58815588-A-G		not specified	Uncertain significance (Jul 06, 2021)
8-58815594-G-A		not specified	Uncertain significance (Apr 08, 2022)
8-58815630-G-A		not specified	Uncertain significance (May 18, 2022)
8-58815703-C-T		not specified	Uncertain significance (Jul 26, 2022)
8-58851539-G-A			Likely benign (Jan 18, 2024)
8-58851690-T-C		not specified	Uncertain significance (Sep 23, 2023)
8-58851695-C-T		not specified	Uncertain significance (Jan 19, 2022)
8-58851809-CAATAAATA-C			Benign (Sep 03, 2018)
8-58939402-C-T		not specified	Uncertain significance (Nov 03, 2023)
8-58939442-A-G		not specified	Likely benign (Oct 21, 2021)
8-58939483-G-A		not specified	Uncertain significance (Nov 20, 2023)
8-58959959-T-C		not specified	Uncertain significance (Feb 23, 2023)
8-58959986-A-G		not specified	Uncertain significance (Feb 03, 2023)
8-59118915-G-C		not specified	Uncertain significance (Dec 02, 2022)
8-59118981-C-G		not specified	Uncertain significance (Oct 10, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TOX	protein_coding	protein_coding	ENST00000361421	9	313791

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.00131	125319	0	2	125321	0.00000798

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.20	240	298	0.804	0.0000148	3473
Missense in Polyphen		103	146.72	0.70201		1767
Synonymous	1.13	102	118	0.868	0.00000692	1018
Loss of Function	4.32	1	23.7	0.0422	0.00000111	269

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000625	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.0000332	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in regulating T-cell development. {ECO:0000250}.
• Pathway: Mesodermal Commitment Pathway;Development and heterogeneity of the ILC family (Consensus)

Recessive Scores

• pRec: 0.200

Intolerance Scores

• loftool: 0.203
• rvis_EVS: -0.62
• rvis_percentile_EVS: 17.31

Haploinsufficiency Scores

• pHI: 0.945
• hipred: Y
• hipred_score: 0.595
• ghis: 0.518

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.855

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tox
• Phenotype: immune system phenotype; digestive/alimentary phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;lymphocyte differentiation;positive regulation of natural killer cell differentiation;lymph node development;Peyer's patch development
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding