TOX2

TOX high mobility group box family member 2, the group of thymocyte selection associated high mobility group box family

Basic information

Region (hg38): 20:43914852-44069616

Previous symbols: [ "C20orf100" ]

Links

ENSG00000124191 ∙ NCBI:84969 ∙ OMIM:611163 ∙ HGNC:16095 ∙ Uniprot:Q96NM4 ∙ 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 TOX2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TOX2 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						0
missense			29	1		30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	30	1	0

Variants in TOX2

This is a list of pathogenic ClinVar variants found in the TOX2 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-43914910-C-T		not specified	Uncertain significance (Sep 15, 2021)
20-43914916-G-T		not specified	Uncertain significance (Jan 04, 2024)
20-43973368-T-C		not specified	Uncertain significance (Jul 06, 2021)
20-43973379-A-G		not specified	Uncertain significance (Oct 25, 2022)
20-43973424-A-G		not specified	Uncertain significance (Mar 01, 2024)
20-44006614-C-T		not specified	Uncertain significance (Aug 13, 2021)
20-44006688-G-A		not specified	Uncertain significance (Jun 01, 2023)
20-44006767-A-G		not specified	Uncertain significance (Feb 10, 2022)
20-44006790-A-G		not specified	Uncertain significance (Sep 07, 2022)
20-44051315-A-G			Likely benign (Apr 23, 2018)
20-44051423-A-T		not specified	Uncertain significance (Jan 24, 2024)
20-44051434-G-A		not specified	Uncertain significance (Aug 01, 2022)
20-44051438-A-G		not specified	Uncertain significance (Jan 26, 2022)
20-44051441-C-T		not specified	Uncertain significance (Feb 15, 2023)
20-44051442-G-A		not specified	Uncertain significance (Jul 22, 2022)
20-44051529-C-T		not specified	Uncertain significance (May 23, 2024)
20-44054303-C-T		not specified	Uncertain significance (Jan 23, 2024)
20-44054313-G-T			Uncertain significance (May 04, 2017)
20-44054317-C-T		not specified	Uncertain significance (Oct 05, 2021)
20-44054357-A-G		not specified	Uncertain significance (Jun 06, 2022)
20-44054473-G-A		not specified	Uncertain significance (Jan 10, 2023)
20-44065796-A-C		not specified	Uncertain significance (May 26, 2023)
20-44065797-T-C		not specified	Uncertain significance (Dec 13, 2022)
20-44065824-C-T		not specified	Uncertain significance (Dec 09, 2023)
20-44065874-C-T		not specified	Uncertain significance (Sep 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TOX2	protein_coding	protein_coding	ENST00000341197	9	154753

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0320	0.966	125737	0	11	125748	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.595	263	292	0.902	0.0000174	3253
Missense in Polyphen		132	164.78	0.80105		1799
Synonymous	0.296	135	139	0.968	0.0000102	1065
Loss of Function	2.75	6	18.9	0.318	8.05e-7	238

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000656	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000934	0.0000924
European (Non-Finnish)	0.0000359	0.0000352
Middle Eastern	0.000109	0.000109
South Asian	0.0000721	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Putative transcriptional activator involved in the hypothalamo-pituitary-gonadal system.
• Pathway: Pathways in clear cell renal cell carcinoma (Consensus)

Recessive Scores

• pRec: 0.0904

Intolerance Scores

• loftool: 0.667
• rvis_EVS: -0.26
• rvis_percentile_EVS: 34.88

Haploinsufficiency Scores

• pHI: 0.542
• hipred: Y
• hipred_score: 0.681
• ghis: 0.459

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.731

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tox2

Gene ontology

• Biological process: positive regulation of transcription by RNA polymerase II
• Cellular component: nucleoplasm
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific