THAP4

protein-coding

THAP domain containing 4, the group of THAP domain containing

Gene summary

Enables several functions, including heme binding activity; nitric oxide binding activity; and peroxynitrite isomerase activity. Involved in nitrate metabolic process and tyrosine metabolic process. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_015963.6

Inheritance

—

ClinVar variants

U:89B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.24

Max pathogenic AF

—

Genomic locus

chr2:241,584,405-241,637,158

External References & Databases

Ensembl (ENSG00000176946)

Transcript & Mutation Effects

hg38 • Region Span ~52.8 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 THAP4 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 87

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015963.6. 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			2 clinvar	1 clinvar		3
missense			84 clinvar	6 clinvar		90
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	89	7	0	96

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 30 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015963.6	RefSeq	NP_057047.4	6	MANE Select
ENST00000407315.6	Ensembl	ENSP00000385006.1	6	MANE Select
NM_001164356.2	RefSeq	NP_001157828.1	5	Standard
ENST00000402136.5	Ensembl	ENSP00000385931.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription by RNA polymerase II
biological_process

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific
DNA binding
heme binding
protein homodimerization activity
metal ion binding

Cellular Component

cellular_component

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000407315
Coding exons: 6
Length: 53045
Individuals with no LoFs: 125738
Homozygous LoFs: 0
Heterozygous LoFs: 6
Defined: 125744
p: 0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.90	261	363	0.719	0.0000226	3741
Missense (PolyPhen)		91	171.46	0.53075		1786
Synonymous	-0.101	164	162	1.01	0.0000117	1187
Loss of Function	3.24	5	21.0	0.238	0.00000115	239

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.000035	0.000035	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.106

Intolerance Scores

LoFtool: 0.0521
RVIS EVS: -0.18
RVIS percentile EVS: 40.45

Essentials

Essential (CRISPR): E
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.493

Gene Damage Prediction

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