THAP10

Summary

THAP10 (THAP domain containing 10, HGNC:23193) is a protein-coding gene on chromosome 15q23, encoding THAP domain-containing protein 10 (Q9P2Z0).

This gene encodes a member of a family of proteins sharing an N-terminal Thanatos-associated domain. The Thanatos-associated domain contains a zinc finger signature similar to DNA-binding domains. This gene is part of a bidirectional gene pair on the long arm of chromosome 15 that is regulated by estrogen and may play a role in breast cancer.

Source: NCBI Gene 56906 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 2 total
• MANE Select transcript: NM_020147

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23193
Approved symbol	THAP10
Name	THAP domain containing 10
Location	15q23
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000129028
Ensembl biotype	protein_coding
OMIM	612538
Entrez	56906

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000249861, ENST00000560604

RefSeq mRNA: 1 — MANE Select: NM_020147 NM_020147

CCDS: CCDS10237

Canonical transcript exons

ENST00000249861 — 3 exons

Exon	Start	End
ENSE00000931727	70891844	70892433
ENSE00001100513	70881342	70882650
ENSE00001100516	70882761	70882908

Expression profiles

Bgee: expression breadth ubiquitous, 234 present calls, max score 89.42.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 3.9279 / max 45.3284, expressed in 1339 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
150741	2.9950	1220
150742	0.5113	304
150743	0.4216	211

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
bronchial epithelial cell	CL:0002328	89.42	gold quality
Brodmann (1909) area 23	UBERON:0013554	87.74	gold quality
oocyte	CL:0000023	87.58	gold quality
secondary oocyte	CL:0000655	87.36	gold quality
primary visual cortex	UBERON:0002436	84.96	gold quality
endothelial cell	CL:0000115	84.35	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	84.00	gold quality
pigmented layer of retina	UBERON:0001782	83.66	gold quality
retina	UBERON:0000966	83.65	gold quality
epithelium of bronchus	UBERON:0002031	83.39	gold quality
bronchus	UBERON:0002185	81.88	gold quality
ventricular zone	UBERON:0003053	81.58	gold quality
sperm	CL:0000019	81.41	silver quality
middle temporal gyrus	UBERON:0002771	81.24	gold quality
postcentral gyrus	UBERON:0002581	80.68	gold quality
prefrontal cortex	UBERON:0000451	80.62	gold quality
ganglionic eminence	UBERON:0004023	79.05	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	78.85	gold quality
male germ cell	CL:0000015	78.79	silver quality
occipital lobe	UBERON:0002021	78.78	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	78.43	gold quality
superior frontal gyrus	UBERON:0002661	78.35	gold quality
adult organism	UBERON:0007023	78.20	gold quality
cortical plate	UBERON:0005343	77.91	gold quality
Brodmann (1909) area 9	UBERON:0013540	77.72	gold quality
frontal cortex	UBERON:0001870	77.61	gold quality
neocortex	UBERON:0001950	77.56	gold quality
mucosa of paranasal sinus	UBERON:0005030	77.02	silver quality
cerebral cortex	UBERON:0000956	76.90	gold quality
Brodmann (1909) area 46	UBERON:0006483	76.87	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.24

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

54 targeting THAP10, 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-4776-3P	100.00	68.73	1340
HSA-MIR-6759-5P	99.99	66.54	785
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-4803	99.98	71.99	3117
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-433-3P	99.98	69.37	1203
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-6835-3P	99.93	70.49	2904
HSA-MIR-5680	99.91	69.83	3421
HSA-MIR-7-1-3P	99.91	71.53	4384
HSA-MIR-7-2-3P	99.91	71.40	4394
HSA-MIR-944	99.82	70.85	3042
HSA-MIR-4422	99.72	72.07	2908
HSA-MIR-1208	99.70	68.28	1533
HSA-MIR-5580-3P	99.70	69.41	2052
HSA-MIR-1284	99.67	73.56	1353
HSA-MIR-7-5P	99.67	70.53	1809
HSA-MIR-6832-5P	99.58	64.82	1132
HSA-MIR-3616-5P	99.55	67.02	989
HSA-MIR-573	99.55	67.44	955
HSA-MIR-3171	99.49	69.06	776
HSA-MIR-3123	99.47	67.15	2693
HSA-MIR-569	99.42	66.32	1009
HSA-MIR-372-5P	99.41	69.11	2299
HSA-MIR-103A-1-5P	99.39	67.78	1545
HSA-MIR-103A-2-5P	99.39	67.72	1577
HSA-MIR-548B-3P	99.38	67.26	1000
HSA-MIR-520F-5P	99.34	70.40	1632

Literature-anchored findings (GeneRIF, showing 2)

• transcripts of LRRC49/THAP10 bidirectional gene pair are co-regulated by estrogen and that hypermethylation of the bidirectional promoter region simultaneously silences both genes. (PMID:18575747)
• Altogether, these results revealed an unexpected and important epigenetic mini-circuit of AML1-ETO/THAP10/miR-383 in t(8;21) acute myeloid leukaemia, in which epigenetic suppression of THAP10 predicts a poor clinical outcome and represents a novel therapeutic target. (PMID:28539478)

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	phc1	ENSDARG00000002971
drosophila_melanogaster	l(3)mbt	FBGN0002441
drosophila_melanogaster	Scm	FBGN0003334
drosophila_melanogaster	Sfmbt	FBGN0032475
caenorhabditis_elegans	lin-61	WBGENE00003041
caenorhabditis_elegans	mbtr-1	WBGENE00021661

Paralogs (18): SCMH1 (ENSG00000010803), MBTD1 (ENSG00000011258), SCML1 (ENSG00000047634), L3MBTL2 (ENSG00000100395), SCML2 (ENSG00000102098), PHC1 (ENSG00000111752), PHC2 (ENSG00000134686), SAMD1 (ENSG00000141858), SCML4 (ENSG00000146285), L3MBTL4 (ENSG00000154655), SFMBT1 (ENSG00000163935), PHC3 (ENSG00000173889), L3MBTL1 (ENSG00000185513), SAMD7 (ENSG00000187033), SAMD11 (ENSG00000187634), SFMBT2 (ENSG00000198879), L3MBTL3 (ENSG00000198945), SAMD13 (ENSG00000203943)

Protein

Protein identifiers

THAP domain-containing protein 10 — Q9P2Z0 (reviewed: Q9P2Z0)

All UniProt accessions (2): Q9P2Z0, H0YN95

RefSeq proteins (1): NP_064532* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR006612	THAP_Znf	Domain
IPR026516	THAP1/10	Family
IPR038441	THAP_Znf_sf	Homologous_superfamily

Pfam: PF05485

UniProt features (4 total): chain 1, zinc finger region 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9P2Z0-F1	63.38	0.25

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 72 (showing top): BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN, NRF2_01, chr15q23, PTF1BETA_Q6, MODULE_95, CETS1P54_01, TTCNRGNNNNTTC_HSF_Q6, NUYTTEN_EZH2_TARGETS_DN, SCGGAAGY_ELK1_02, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, MODULE_49, PHONG_TNF_RESPONSE_NOT_VIA_P38, BONOME_OVARIAN_CANCER_SURVIVAL_SUBOPTIMAL_DEBULKING, MODULE_163, IL2_UP.V1_DN

GO Biological Process (0):

GO Molecular Function (5): zinc ion binding (GO:0008270), sequence-specific DNA binding (GO:0043565), DNA binding (GO:0003677), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
transition metal ion binding	1
DNA binding	1
nucleic acid binding	1
binding	1
cation binding	1

Protein interactions and networks

STRING

230 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
THAP10	THAP8	Q8NA92	697
THAP10	LRRC49	Q8IUZ0	603
THAP10	THAP9	Q9H5L6	599
THAP10	THAP12	O43422	592
THAP10	THAP6	Q8TBB0	588
THAP10	THAP5	Q7Z6K1	583
THAP10	THAP4	Q8WY91	571
THAP10	THAP3	Q8WTV1	570
THAP10	THAP11	Q96EK4	570
THAP10	THAP7	Q9BT49	549
THAP10	THAP1	Q9NVV9	519
THAP10	THAP2	Q9H0W7	507
THAP10	DYNLL2	Q96FJ2	466
THAP10	DNAL4	O96015	419
THAP10	SURF2	Q15527	400

IntAct

48 interactions, top by confidence:

A	B	Type	Score
THAP10	CCNDBP1	psi-mi:“MI:0915”(physical association)	0.740
KRTAP10-5	THAP10	psi-mi:“MI:0915”(physical association)	0.560
THAP10	KRTAP10-8	psi-mi:“MI:0915”(physical association)	0.560
THAP10	KRTAP10-9	psi-mi:“MI:0915”(physical association)	0.560
THAP10	PTS	psi-mi:“MI:0915”(physical association)	0.560
LZTS2	THAP10	psi-mi:“MI:0915”(physical association)	0.560
	THAP10	psi-mi:“MI:0915”(physical association)	0.560
THAP10	KRTAP10-5	psi-mi:“MI:0915”(physical association)	0.560
KRTAP10-8	THAP10	psi-mi:“MI:0915”(physical association)	0.560
THAP10		psi-mi:“MI:0915”(physical association)	0.560
KRTAP10-9	THAP10	psi-mi:“MI:0915”(physical association)	0.560
THAP10	LZTS2	psi-mi:“MI:0915”(physical association)	0.560
THAP10	PLEKHF2	psi-mi:“MI:0915”(physical association)	0.560
PSME3	THAP10	psi-mi:“MI:0915”(physical association)	0.560
THAP10	NME7	psi-mi:“MI:0915”(physical association)	0.560
PLEKHF2	THAP10	psi-mi:“MI:0915”(physical association)	0.560
DYNLL1	THAP10	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (30): THAP10 (Two-hybrid), THAP10 (Two-hybrid), LZTS2 (Two-hybrid), KRTAP10-9 (Two-hybrid), KRTAP10-5 (Two-hybrid), KRTAP10-8 (Two-hybrid), KRTAP10-3 (Two-hybrid), TP53BP1 (Affinity Capture-MS), KRTAP4-12 (Two-hybrid), DYNLL2 (Two-hybrid), THAP10 (Two-hybrid), TP53BP1 (Affinity Capture-MS), THAP10 (Two-hybrid), PSME3 (Two-hybrid), NME7 (Two-hybrid)

ESM2 similar proteins: A4IGQ8, B0BLU1, B5XCB8, O75113, O75132, P14629, Q0IIM1, Q0V8G8, Q17RS7, Q1JPT7, Q1RMM0, Q28GK6, Q28J92, Q3T0G1, Q4R3Q6, Q4R7M0, Q4V7W2, Q5FWF4, Q5NVM3, Q5QJC4, Q5RCE4, Q5SZJ8, Q5U208, Q5U560, Q5ZHN5, Q6A037, Q6DDT6, Q6DIN8, Q6INS5, Q6IR68, Q6NZP1, Q6PFX2, Q6TGZ4, Q7Z6K1, Q7ZYM8, Q80XJ2, Q86VD1, Q8BMI4, Q8BZ05, Q8C4P0

Diamond homologs: Q5NVM3, Q9P2Z0

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	2
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

289 predictions. Top by Δscore:

Variant	Effect	Δscore
15:70882648:TAC:T	acceptor_gain	1.0000
15:70882648:TACC:T	acceptor_loss	1.0000
15:70882651:C:CC	acceptor_gain	1.0000
15:70882651:CTGA:C	acceptor_loss	1.0000
15:70882759:AC:A	donor_gain	1.0000
15:70882760:CC:C	donor_gain	1.0000
15:70882760:CCCA:C	donor_gain	1.0000
15:70882646:AATAC:A	acceptor_gain	0.9900
15:70882647:ATAC:A	acceptor_gain	0.9900
15:70882649:AC:A	acceptor_gain	0.9900
15:70882650:CC:C	acceptor_gain	0.9900
15:70882652:T:A	acceptor_loss	0.9900
15:70882754:AACAT:A	donor_loss	0.9900
15:70882755:ACAT:A	donor_loss	0.9900
15:70882756:CATAC:C	donor_loss	0.9900
15:70882757:ATACC:A	donor_loss	0.9900
15:70882758:T:TG	donor_loss	0.9900
15:70882759:A:AC	donor_gain	0.9900
15:70882759:ACCC:A	donor_loss	0.9900
15:70882760:C:CC	donor_gain	0.9900
15:70882760:C:G	donor_loss	0.9900
15:70882764:CA:C	donor_gain	0.9900
15:70882905:TAAT:T	acceptor_gain	0.9900
15:70882905:TAATC:T	acceptor_loss	0.9900
15:70882907:ATCTA:A	acceptor_loss	0.9900
15:70882908:TC:T	acceptor_loss	0.9900
15:70882909:C:CC	acceptor_gain	0.9900
15:70882909:C:T	acceptor_loss	0.9900
15:70882910:T:G	acceptor_loss	0.9900
15:70882764:CACTA:C	donor_gain	0.9800

AlphaMissense

1660 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
15:70892099:A:C	F58L	0.998
15:70892099:A:T	F58L	0.998
15:70892101:A:G	F58L	0.998
15:70892204:A:C	F23L	0.998
15:70892204:A:T	F23L	0.998
15:70892206:A:G	F23L	0.998
15:70892084:A:C	F63L	0.997
15:70892084:A:T	F63L	0.997
15:70892086:A:G	F63L	0.997
15:70892174:C:A	W33C	0.997
15:70892174:C:G	W33C	0.997
15:70892176:A:G	W33R	0.997
15:70892176:A:T	W33R	0.997
15:70892210:G:C	F21L	0.997
15:70892210:G:T	F21L	0.997
15:70892212:A:G	F21L	0.997
15:70892100:A:G	F58S	0.996
15:70892205:A:G	F23S	0.996
15:70892141:C:A	W44C	0.995
15:70892141:C:G	W44C	0.995
15:70892165:G:C	F36L	0.995
15:70892165:G:T	F36L	0.995
15:70892167:A:G	F36L	0.995
15:70892205:A:C	F23C	0.995
15:70892211:A:G	F21S	0.995
15:70892102:G:C	H57Q	0.994
15:70892102:G:T	H57Q	0.994
15:70892115:A:T	I53N	0.993
15:70892175:C:G	W33S	0.993
15:70892013:G:T	P87H	0.992

dbSNP variants (sampled 300 via entrez): RS1000137025 (15:70882124 T>C), RS1000235905 (15:70885706 C>A,T), RS1000247061 (15:70885999 T>C), RS1000288174 (15:70888908 C>T), RS1000406181 (15:70889346 A>C), RS1000419796 (15:70882123 G>A), RS1000875574 (15:70881652 A>T), RS1001164898 (15:70893208 T>A,C), RS1001920064 (15:70884541 C>A,T), RS1001964070 (15:70890683 G>A), RS1002078829 (15:70890979 A>C,G), RS1002146210 (15:70883432 G>C), RS1002438889 (15:70891750 T>G), RS1002475413 (15:70888884 G>T), RS1002646652 (15:70881559 T>C)

Disease associations

OMIM: gene MIM:612538 | 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
GCST010396_103	Gut microbiota (bacterial taxa, hurdle binary method)	4.000000e-07

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0007874	gut microbiome measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

23 total (human), top 23 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	increases expression	3
Valproic Acid	affects expression, increases expression	3
Aflatoxin B1	affects expression, increases expression, increases methylation	3
Air Pollutants	increases abundance, increases expression, decreases expression	2
Nickel	decreases expression	2
Cyclosporine	affects expression, increases expression	2
Particulate Matter	increases abundance, increases expression, decreases expression	2
aristolochic acid I	increases expression	1
benzo(e)pyrene	increases methylation	1
beta-methylcholine	affects expression	1
Sunitinib	decreases expression	1
Atrazine	decreases expression	1
Cisplatin	increases expression	1
Ethyl Methanesulfonate	increases expression	1
Formaldehyde	increases expression	1
Methapyrilene	increases methylation	1
Methyl Methanesulfonate	increases expression	1
Quercetin	increases expression	1
Tretinoin	decreases expression	1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	increases expression	1
Antirheumatic Agents	increases expression	1
Cadmium Chloride	decreases expression	1
Acrylamide	increases expression	1

Cellosaurus cell lines

3 cell lines: 3 embryonic stem cell

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_A7K8	SEES3-1V human THAP10, clone1	Embryonic stem cell	Male
CVCL_A7K9	SEES3-1V human THAP10, clone2	Embryonic stem cell	Male
CVCL_A7L0	SEES3-1V human THAP10, clone3	Embryonic stem cell	Male

Clinical trials (associated diseases)

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