THAP9

protein-coding

THAP domain containing 9, the group of THAP domain containing

Gene summary

Enables sequence-specific DNA binding activity and transposase activity. Involved in DNA integration and DNA transposition. Predicted to be located in nucleoplasm. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_024672.6

Inheritance

—

ClinVar variants

U:107B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.7

Max pathogenic AF

—

Genomic locus

chr4:82,900,684-82,919,969

External References & Databases

Ensembl (ENSG00000168152)

Transcript & Mutation Effects

hg38 • Region Span ~19.3 kb

Loading mutation effect viewer...

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 THAP9 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 110

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024672.6. 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				1 clinvar		1
missense			106 clinvar	4 clinvar		110
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	107	5	0	112

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 14 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024672.6	RefSeq	NP_078948.3	5	MANE Select
ENST00000302236.10	Ensembl	ENSP00000305533.5	5	MANE Select
NM_001317776.2	RefSeq	NP_001304705.1	3	Standard
ENST00000505901.1	Ensembl	ENSP00000425966.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

DNA recombination
transposition, DNA-mediated
regulation of transcription by RNA polymerase II
DNA integration

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific
transposase activity
transferase activity
sequence-specific DNA binding
metal ion binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000302236
Coding exons: 5
Length: 19286
Individuals with no LoFs: 125619
Homozygous LoFs: 0
Heterozygous LoFs: 129
Defined: 125748
p: 0.000513

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.44	370	457	0.810	0.0000221	5945
Missense (PolyPhen)		67	118.51	0.56537		1549
Synonymous	0.925	153	168	0.909	0.00000819	1699
Loss of Function	1.65	24	34.5	0.697	0.00000199	434

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0010	0.00098	rare
Latino/Admixed American	0.00035	0.00035	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.0017	0.0017	notable
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00029	0.00028	rare
South Asian	0.00099	0.00098	rare
Other	0.00052	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Active transposase that specifically recognizes the bipartite 5'-TXXGGGX(A/T)-3' consensus motif and mediates transposition. {ECO:0000269|PubMed:20010837, ECO:0000269|PubMed:23349291}.;

Recessive Scores

pRec: 0.0934

Intolerance Scores

LoFtool: 0.275
RVIS EVS: 0.62
RVIS percentile EVS: 83.53

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0618

Gene Damage Prediction

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