THAP7

protein-coding

THAP domain containing 7, the group of THAP domain containing

Gene summary

Enables several functions, including C2H2 zinc finger domain binding activity; histone deacetylase binding activity; and transcription corepressor binding activity. Involved in chromatin organization and negative regulation of transcription by RNA polymerase II. Located in chromatin and nuclear speck. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_030573.3

Inheritance

—

ClinVar variants

U:52

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.41

Max pathogenic AF

—

Genomic locus

chr22:20,999,104-21,002,196

External References & Databases

Ensembl (ENSG00000184436)

Transcript & Mutation Effects

hg38 • Region Span ~3.1 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 THAP7 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 50

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_030573.3. 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			51 clinvar			51
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	52	0	0	52

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 8 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_030573.3	RefSeq	NP_085050.2	4	MANE Select
ENST00000215742.9	Ensembl	ENSP00000215742.4	4	MANE Select
NM_001008695.1	RefSeq	NP_001008695.1	4	Standard
ENST00000399133.2	Ensembl	ENSP00000382084.2	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription by RNA polymerase II
negative regulation of transcription, DNA-templated

Molecular Function

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

Cellular Component

nucleus
chromosome
nuclear speck
nuclear membrane
intracellular membrane-bounded organelle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000215742
Coding exons: 4
Length: 3093
Individuals with no LoFs: 125738
Homozygous LoFs: 0
Heterozygous LoFs: 8
Defined: 125746
p: 0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.385	171	186	0.921	0.0000114	1917
Missense (PolyPhen)		38	53.274	0.7133		531
Synonymous	-2.20	99	74.8	1.32	0.00000401	658
Loss of Function	1.90	5	12.2	0.411	6.62e-7	137

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000026	0.000026	rare
South Asian	0.000033	0.000033	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Chromatin-associated, histone tail-binding protein that represses transcription via recruitment of HDAC3 and nuclear hormone receptor corepressors. {ECO:0000269|PubMed:15561719}.;

Recessive Scores

pRec: 0.110

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): H
Indispensability pred.: E
Indispensability score: 1.00

Gene Damage Prediction

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