TOX4

protein-coding

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

Gene summary

Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific and chromatin DNA binding activity. Involved in RNA polymerase II promoter clearance and positive regulation of transcription elongation by RNA polymerase II. Located in chromatin and chromosome, telomeric region. Part of PTW/PP1 phosphatase complex. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

C14orf92
KIAA0737

MANE transcript

NM_014828.4

Inheritance

—

ClinVar variants

U:67B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.15

Max pathogenic AF

—

Genomic locus

chr14:21,476,597-21,499,175

External References & Databases

Ensembl (ENSG00000092203)

Transcript & Mutation Effects

hg38 • Region Span ~22.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TOX4 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 65

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014828.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar			1
missense			63 clinvar	2 clinvar		65
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	67	2	0	69

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 43 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014828.4	RefSeq	NP_055643.1	9	MANE Select
ENST00000448790.7	Ensembl	ENSP00000393080.3	9	MANE Select
NM_001303523.2	RefSeq	NP_001290452.1	8	Standard
ENST00000416256.5	Ensembl	ENSP00000402195.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription by RNA polymerase II

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific
DNA binding
protein binding

Cellular Component

nuclear chromosome, telomeric region
chromatin
PTW/PP1 phosphatase complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000405508
Coding exons: 9
Length: 22564
Individuals with no LoFs: 125734
Homozygous LoFs: 0
Heterozygous LoFs: 11
Defined: 125745
p: 0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.37	213	335	0.635	0.0000160	4017
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00011	0.00011	rare
Finnish	0.000093	0.000092	rare
European (Non-Finnish)	0.000044	0.000044	rare
South Asian	0	0.0	absent
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Indispensability pred.: E
Indispensability score: 0.951

Gene Damage Prediction

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