TOX4

TOX high mobility group box family member 4, the group of thymocyte selection associated high mobility group box family

Basic information

Region (hg38): 14:21476597-21499175

Previous symbols: [ "C14orf92", "KIAA0737" ]

Links

ENSG00000092203 ∙ NCBI:9878 ∙ OMIM:614032 ∙ HGNC:20161 ∙ Uniprot:O94842 ∙ 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 TOX4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TOX4 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			30	2		32
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	31	2	0

Variants in TOX4

This is a list of pathogenic ClinVar variants found in the TOX4 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-21477544-C-G		not specified	Uncertain significance (Jun 16, 2023)
14-21487497-C-A		not specified	Uncertain significance (Jun 09, 2022)
14-21487589-A-C		not specified	Uncertain significance (Dec 21, 2022)
14-21488605-A-G		not specified	Uncertain significance (Jul 17, 2023)
14-21488606-T-C		not specified	Uncertain significance (Dec 28, 2023)
14-21488747-G-C		not specified	Uncertain significance (Dec 22, 2023)
14-21488786-G-C		not specified	Uncertain significance (May 08, 2023)
14-21488795-C-A		not specified	Uncertain significance (Jun 06, 2023)
14-21488846-G-T		not specified	Uncertain significance (Apr 23, 2024)
14-21489188-A-C		not specified	Uncertain significance (Jun 17, 2024)
14-21489194-G-A		not specified	Uncertain significance (Nov 08, 2022)
14-21489248-G-A		not specified	Uncertain significance (Nov 08, 2022)
14-21492350-G-A		not specified	Uncertain significance (Apr 25, 2022)
14-21492562-C-T		not specified	Uncertain significance (Aug 04, 2023)
14-21492610-A-G		not specified	Uncertain significance (Sep 22, 2022)
14-21492667-G-A		not specified	Uncertain significance (Sep 17, 2021)
14-21492707-A-G		not specified	Uncertain significance (Jun 12, 2023)
14-21492757-A-G		not specified	Uncertain significance (Nov 28, 2023)
14-21492858-A-C		not specified	Uncertain significance (Nov 13, 2023)
14-21492902-C-T		not specified	Uncertain significance (Oct 03, 2022)
14-21492931-C-G		not specified	Uncertain significance (Nov 23, 2021)
14-21492931-C-T		not specified	Uncertain significance (May 13, 2024)
14-21492941-G-A		not specified	Uncertain significance (Jun 10, 2022)
14-21493040-C-T		not specified	Uncertain significance (Aug 01, 2022)
14-21493058-G-T		not specified	Uncertain significance (May 14, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TOX4	protein_coding	protein_coding	ENST00000405508	9	22564

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.956	0.0436	125734	0	11	125745	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.37	213	335	0.635	0.0000160	4017
Missense in Polyphen		48	106.84	0.44926		1393
Synonymous	-0.0209	123	123	1.00	0.00000566	1305
Loss of Function	4.15	4	27.4	0.146	0.00000140	307

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000109	0.000109
Finnish	0.0000932	0.0000924
European (Non-Finnish)	0.0000441	0.0000440
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the PTW/PP1 phosphatase complex, which plays a role in the control of chromatin structure and cell cycle progression during the transition from mitosis into interphase. {ECO:0000269|PubMed:20516061}.

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.330
• rvis_EVS: -0.36
• rvis_percentile_EVS: 28.93

Haploinsufficiency Scores

• pHI: 0.768
• hipred: Y
• hipred_score: 0.565
• ghis: 0.613

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• gene_indispensability_pred: E
• gene_indispensability_score: 0.951

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tox4

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II
• Cellular component: nuclear chromosome, telomeric region;chromatin;PTW/PP1 phosphatase complex
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;protein binding