THAP2

Summary

THAP2 (THAP domain containing 2, HGNC:20854) is a protein-coding gene on chromosome 12q21.1, encoding THAP domain-containing protein 2 (Q9H0W7).

Predicted to enable DNA binding activity and zinc ion binding activity. Located in nucleolus.

Source: NCBI Gene 83591 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 34 total
• MANE Select transcript: NM_031435

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20854
Approved symbol	THAP2
Name	THAP domain containing 2
Location	12q21.1
Locus type	gene with protein product
Status	Approved
Aliases	DKFZP564I0422
Ensembl gene	ENSG00000173451
Ensembl biotype	protein_coding
OMIM	612531
Entrez	83591

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 4 protein_coding

ENST00000308086, ENST00000547843, ENST00000551238, ENST00000551488

RefSeq mRNA: 1 — MANE Select: NM_031435 NM_031435

CCDS: CCDS9001

Canonical transcript exons

ENST00000308086 — 3 exons

Exon	Start	End
ENSE00001194720	71664301	71664580
ENSE00001322300	71676689	71680644
ENSE00003554985	71674203	71674398

Expression profiles

Bgee: expression breadth ubiquitous, 200 present calls, max score 87.61.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 10.1984 / max 143.5361, expressed in 1762 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
126821	4.0689	1556
126818	2.7381	1211
126819	2.1647	1028
126820	1.2167	678
126822	0.0101	3

Top tissues by expression

253 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
cortical plate	UBERON:0005343	87.61	gold quality
embryo	UBERON:0000922	87.33	gold quality
ganglionic eminence	UBERON:0004023	87.33	gold quality
ventricular zone	UBERON:0003053	84.66	gold quality
left testis	UBERON:0004533	83.92	gold quality
right testis	UBERON:0004534	83.59	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.22	gold quality
lower esophagus mucosa	UBERON:0035834	82.40	gold quality
testis	UBERON:0000473	81.81	gold quality
adrenal tissue	UBERON:0018303	80.59	gold quality
monocyte	CL:0000576	80.41	gold quality
adenohypophysis	UBERON:0002196	80.40	gold quality
leukocyte	CL:0000738	80.16	gold quality
vermiform appendix	UBERON:0001154	79.94	gold quality
pituitary gland	UBERON:0000007	79.82	gold quality
right uterine tube	UBERON:0001302	79.74	gold quality
gall bladder	UBERON:0002110	79.03	gold quality
mucosa of transverse colon	UBERON:0004991	79.03	gold quality
right hemisphere of cerebellum	UBERON:0014890	79.01	gold quality
esophagus mucosa	UBERON:0002469	78.97	gold quality
cerebellar hemisphere	UBERON:0002245	78.91	gold quality
cerebellar cortex	UBERON:0002129	78.74	gold quality
islet of Langerhans	UBERON:0000006	78.67	gold quality
left adrenal gland cortex	UBERON:0035825	78.60	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	78.13	gold quality
adrenal gland	UBERON:0002369	78.07	gold quality
left adrenal gland	UBERON:0001234	77.68	gold quality
cerebellum	UBERON:0002037	77.42	gold quality
calcaneal tendon	UBERON:0003701	77.33	gold quality
right adrenal gland cortex	UBERON:0035827	77.32	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

179 targeting THAP2, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-4682	100.00	68.89	1258
HSA-MIR-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-9-5P	100.00	72.28	2361
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-29B-3P	100.00	73.18	1833
HSA-MIR-29C-3P	100.00	73.15	1833
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-29A-3P	100.00	73.11	1835
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-4482-3P	99.98	72.50	3147
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-6891-5P	99.98	66.53	1372
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-6793-5P	99.97	65.95	758
HSA-MIR-2110	99.96	66.68	1930

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	zgc:153292	ENSDARG00000070458
danio_rerio		ENSDARG00000076082
danio_rerio	zgc:163143	ENSDARG00000076437
mus_musculus	Thap2	ENSMUSG00000020137
rattus_norvegicus	Thap2	ENSRNOG00000080951
drosophila_melanogaster	CG13894	FBGN0035157

Paralogs (7): THAP3 (ENSG00000041988), THAP1 (ENSG00000131931), ARL14EP (ENSG00000152219), THAP8 (ENSG00000161277), THAP6 (ENSG00000174796), THAP7 (ENSG00000184436), ARL14EPL (ENSG00000268223)

Protein

Protein identifiers

THAP domain-containing protein 2 — Q9H0W7 (reviewed: Q9H0W7)

All UniProt accessions (4): Q9H0W7, F8VW94, F8VYP5, F8W1B8

RefSeq proteins (1): NP_113623* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR006612	THAP_Znf	Domain
IPR026521	THAP2	Family
IPR038441	THAP_Znf_sf	Homologous_superfamily

Pfam: PF05485

UniProt features (7 total): strand 2, chain 1, zinc finger region 1, short sequence motif 1, sequence variant 1, helix 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
2D8R	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9H0W7-F1	75.63	0.30

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 113 (showing top): GTGCCTT_MIR506, chr12q21, NIKOLSKY_BREAST_CANCER_12Q13_Q21_AMPLICON, DODD_NASOPHARYNGEAL_CARCINOMA_UP, CUI_TCF21_TARGETS_2_DN, TGCCTTA_MIR124A, GOCC_NUCLEOLUS, ASGHARZADEH_NEUROBLASTOMA_POOR_SURVIVAL_DN, OCT_Q6, ARNT2_TARGET_GENES, ATF5_TARGET_GENES, BANP_TARGET_GENES, BARX1_TARGET_GENES, CIITA_TARGET_GENES, DYRK1A_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (3): DNA binding (GO:0003677), zinc ion binding (GO:0008270), metal ion binding (GO:0046872)

GO Cellular Component (2): nucleus (GO:0005634), nucleolus (GO:0005730)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
nucleic acid binding	1
transition metal ion binding	1
cation binding	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
intracellular membraneless organelle	1

Protein interactions and networks

STRING

314 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
THAP2	THAP11	Q96EK4	890
THAP2	PAWR	Q96IZ0	528
THAP2	THAP10	Q9P2Z0	507
THAP2	RRM1	P23921	481
THAP2	RBM12B	Q8IXT5	446
THAP2	BAZ2A	Q9UIF9	385
THAP2	ZNF215	Q9UL58	368
THAP2	CYRIA	Q9H0Q0	357
THAP2	FEM1B	Q9UK73	349
THAP2	THAP12	O43422	346
THAP2	TAF1B	Q53T94	340
THAP2	THAP7	Q9BT49	339
THAP2	THAP4	Q8WY91	333
THAP2	RBM3	P98179	328
THAP2	THAP3	Q8WTV1	311

IntAct

5 interactions, top by confidence:

A	B	Type	Score
THAP2	OGT	psi-mi:“MI:0914”(association)	0.530
THAP2	VANGL1	psi-mi:“MI:0915”(physical association)	0.370
THAP2	PTPN12	psi-mi:“MI:0915”(physical association)	0.370

BioGRID (23): HCFC1 (Affinity Capture-MS), HCFC2 (Affinity Capture-MS), CTNNBL1 (Affinity Capture-MS), TRIM71 (Affinity Capture-MS), DNAJB8 (Affinity Capture-MS), CTNNBL1 (Affinity Capture-MS), TRIM71 (Affinity Capture-MS), DNAJB8 (Affinity Capture-MS), HCFC2 (Affinity Capture-MS), OGT (Affinity Capture-MS), HCFC1 (Affinity Capture-MS), THAP2 (Synthetic Lethality), THAP2 (Proximity Label-MS), DNAJB8 (Affinity Capture-MS), HCFC1 (Affinity Capture-MS)

ESM2 similar proteins: A4IFA3, A4Z943, A4Z944, A4Z945, B2RRL2, D3Z4R1, F1NQJ3, O43422, O60108, O60290, O96006, P08770, P0CF97, P12258, P16320, P34601, Q09772, Q0VBL1, Q17RP2, Q3EBC8, Q3YK19, Q49AG3, Q4R6P1, Q4W5G0, Q5SVZ6, Q5SXJ3, Q6EKJ0, Q6NT04, Q6R2W3, Q7L775, Q7M3K2, Q86UP8, Q8BUZ3, Q8IY51, Q8IZ13, Q8TBB0, Q8TCP9, Q8TDG4, Q8VEH5, Q95M72

Diamond homologs: B5XCB8, Q0IHI7, Q0P5B4, Q1JPT7, Q1RMM0, Q2TBI2, Q3T0G1, Q4R3Q6, Q4R7M0, Q5RCE4, Q5U208, Q5U560, Q5ZHN5, Q642B6, Q6DDT6, Q6DIN8, Q6P3Z3, Q7Z6K1, Q8BJ25, Q8CHW1, Q8WTV1, Q8WY91, Q9D305, Q9H0W7, Q9NVV9, Q9H5L6, Q8NA92, Q8VCZ3, Q9BT49, A0PT73, A0QIQ0, A0R6J8, A1KM55, A1T297, A3PTJ4, A5U669, B2HLY1, O64527, P9WFG6, P9WFG7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

34 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	27
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

406 predictions. Top by Δscore:

Variant	Effect	Δscore
12:71674201:A:G	acceptor_gain	0.9800
12:71674395:TATG:T	donor_loss	0.9800
12:71674396:ATG:A	donor_loss	0.9800
12:71674397:TG:T	donor_loss	0.9800
12:71674398:GG:G	donor_loss	0.9800
12:71674399:G:T	donor_loss	0.9800
12:71676678:ATTC:A	acceptor_gain	0.9800
12:71679513:C:A	acceptor_gain	0.9800
12:71674399:G:GG	donor_gain	0.9700
12:71676659:T:G	acceptor_gain	0.9700
12:71676681:C:CA	acceptor_gain	0.9700
12:71679588:GC:G	donor_gain	0.9700
12:71674406:A:AG	donor_gain	0.9600
12:71676672:A:AG	acceptor_gain	0.9600
12:71674351:G:GT	donor_gain	0.9500
12:71674400:T:A	donor_gain	0.9400
12:71676678:A:AG	acceptor_gain	0.9400
12:71676678:ATTCG:A	acceptor_gain	0.9400
12:71674396:ATGGT:A	donor_gain	0.9300
12:71676682:G:A	acceptor_gain	0.9300
12:71674398:GGT:G	donor_gain	0.9200
12:71664576:CACAG:C	donor_loss	0.9100
12:71664577:ACAG:A	donor_loss	0.9100
12:71664578:CAG:C	donor_loss	0.9100
12:71664579:AG:A	donor_loss	0.9100
12:71664580:GGT:G	donor_loss	0.9100
12:71664581:GTAA:G	donor_loss	0.9100
12:71664582:T:A	donor_loss	0.9100
12:71674399:GT:G	donor_gain	0.9100
12:71676673:A:G	acceptor_gain	0.9000

AlphaMissense

1515 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:71664522:T:C	C5R	1.000
12:71664576:C:G	H23D	1.000
12:71674205:T:C	F25S	1.000
12:71674234:T:A	W35R	1.000
12:71674234:T:C	W35R	1.000
12:71674235:G:C	W35S	1.000
12:71674236:G:C	W35C	1.000
12:71674236:G:T	W35C	1.000
12:71674288:T:A	C53S	1.000
12:71674288:T:C	C53R	1.000
12:71674289:G:C	C53S	1.000
12:71674300:T:C	F57L	1.000
12:71674301:T:C	F57S	1.000
12:71674301:T:G	F57C	1.000
12:71674302:T:A	F57L	1.000
12:71674302:T:G	F57L	1.000
12:71674343:T:A	L71H	1.000
12:71674360:C:A	P77T	1.000
12:71674360:C:T	P77S	1.000
12:71674361:C:A	P77Q	1.000
12:71674361:C:G	P77R	1.000
12:71664522:T:A	C5S	0.999
12:71664523:G:A	C5Y	0.999
12:71664523:G:C	C5S	0.999
12:71664524:C:G	C5W	0.999
12:71664537:T:C	C10R	0.999
12:71664570:A:C	S21R	0.999
12:71664572:C:A	S21R	0.999
12:71664572:C:G	S21R	0.999
12:71664573:T:C	F22L	0.999

dbSNP variants (sampled 300 via entrez): RS1000008631 (12:71667745 G>T), RS1000239142 (12:71675263 T>C,G), RS1000490914 (12:71668071 C>T), RS1000879646 (12:71668059 C>T), RS1001014850 (12:71667758 T>G), RS1001092150 (12:71674925 C>A,T), RS1001177983 (12:71662685 T>C), RS1001353126 (12:71666414 G>A), RS1001652717 (12:71677255 A>G,T), RS1001823196 (12:71673252 A>G), RS1001864391 (12:71680289 T>C), RS1001915141 (12:71679696 A>C), RS1002273585 (12:71663925 C>G,T), RS1002303868 (12:71671132 C>T), RS1002385230 (12:71669823 G>A)

Disease associations

OMIM: gene MIM:612531 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST001511_9	Economic and political preferences (time)	5.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004827	economic and social preference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

41 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, affects expression, decreases methylation	8
trichostatin A	decreases expression, increases expression, affects cotreatment	3
Benzo(a)pyrene	increases expression	3
entinostat	decreases expression, affects cotreatment	2
Aflatoxin B1	decreases methylation, increases expression	2
aristolochic acid I	increases expression	1
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	increases expression	1
GSK-J4	decreases expression	1
TL8-506	affects cotreatment, increases expression	1
methylmercuric chloride	decreases expression	1
2-methyl-4-isothiazolin-3-one	increases expression	1
sodium arsenite	increases expression	1
butyraldehyde	decreases expression	1
lei gong teng	increases expression	1
epigallocatechin gallate	increases expression	1
di-n-butylphosphoric acid	affects expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
abrine	increases expression	1
2,2’,4,4’-tetrabromodiphenyl ether	increases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
jinfukang	affects cotreatment, decreases expression	1
Panobinostat	affects cotreatment, decreases expression	1
Cisplatin	affects cotreatment, decreases expression	1
Clorgyline	increases expression	1
Succimer	increases expression, affects cotreatment	1
Estradiol	decreases expression	1
Formaldehyde	increases expression	1
Phthalic Acids	increases methylation	1
Poly I-C	affects cotreatment, increases expression	1
Quercetin	increases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.