THYN1

Summary

THYN1 (thymocyte nuclear protein 1, HGNC:29560) is a protein-coding gene on chromosome 11q25, encoding Thymocyte nuclear protein 1 (Q9P016). Specifically binds 5-hydroxymethylcytosine (5hmC), suggesting that it acts as a specific reader of 5hmC.

This gene encodes a protein that is highly conserved among vertebrates and plant species and may be involved in the induction of apoptosis. Alternatively spliced transcript variants encoding different isoforms have been described.

Source: NCBI Gene 29087 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 50 total
• MANE Select transcript: NM_014174

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29560
Approved symbol	THYN1
Name	thymocyte nuclear protein 1
Location	11q25
Locus type	gene with protein product
Status	Approved
Aliases	THY28
Ensembl gene	ENSG00000151500
Ensembl biotype	protein_coding
OMIM	613739
Entrez	29087

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 6 protein_coding, 3 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000341541, ENST00000352327, ENST00000392594, ENST00000392595, ENST00000525677, ENST00000531135, ENST00000533781, ENST00000533975, ENST00000948715, ENST00000948716

RefSeq mRNA: 5 — MANE Select: NM_014174 NM_001037304, NM_001037305, NM_014174, NM_199297, NM_199298

CCDS: CCDS8496, CCDS8497

Canonical transcript exons

ENST00000341541 — 7 exons

Exon	Start	End
ENSE00000999994	134248809	134248959
ENSE00000999995	134249167	134249262
ENSE00002154212	134252840	134253352
ENSE00003499209	134249828	134249920
ENSE00003512780	134251130	134251308
ENSE00003533917	134250275	134250343
ENSE00003842511	134248282	134248484

Expression profiles

Bgee: expression breadth ubiquitous, 287 present calls, max score 98.04.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 27.3406 / max 224.4737, expressed in 1803 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
123262	27.3406	1803

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
oocyte	CL:0000023	98.04	gold quality
right hemisphere of cerebellum	UBERON:0014890	97.27	gold quality
cerebellar hemisphere	UBERON:0002245	97.25	gold quality
cerebellar cortex	UBERON:0002129	97.22	gold quality
right frontal lobe	UBERON:0002810	96.98	gold quality
adenohypophysis	UBERON:0002196	96.78	gold quality
cerebellum	UBERON:0002037	96.68	gold quality
Brodmann (1909) area 9	UBERON:0013540	96.59	gold quality
nucleus accumbens	UBERON:0001882	96.58	gold quality
left ovary	UBERON:0002119	96.58	gold quality
anterior cingulate cortex	UBERON:0009835	96.56	gold quality
cingulate cortex	UBERON:0003027	96.55	gold quality
ganglionic eminence	UBERON:0004023	96.50	gold quality
right ovary	UBERON:0002118	96.49	gold quality
caudate nucleus	UBERON:0001873	96.45	gold quality
pituitary gland	UBERON:0000007	96.36	gold quality
amygdala	UBERON:0001876	96.35	gold quality
ventricular zone	UBERON:0003053	96.26	gold quality
putamen	UBERON:0001874	96.17	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	96.12	gold quality
muscle layer of sigmoid colon	UBERON:0035805	96.06	gold quality
right uterine tube	UBERON:0001302	95.98	gold quality
body of uterus	UBERON:0009853	95.85	gold quality
prefrontal cortex	UBERON:0000451	95.84	gold quality
mucosa of stomach	UBERON:0001199	95.83	gold quality
descending thoracic aorta	UBERON:0002345	95.83	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	95.79	gold quality
cerebellar vermis	UBERON:0004720	95.72	gold quality
lower esophagus muscularis layer	UBERON:0035833	95.66	gold quality
neocortex	UBERON:0001950	95.65	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-CURD-135	no	816.36
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

18 targeting THYN1, 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-12136	99.98	72.81	5713
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-7162-3P	99.89	68.16	1682
HSA-MIR-548D-3P	99.87	70.67	4362
HSA-MIR-548BB-3P	99.86	70.58	4354
HSA-MIR-548AC	99.84	70.77	4351
HSA-MIR-548H-3P	99.84	70.80	4349
HSA-MIR-548Z	99.84	70.80	4349
HSA-MIR-4530	99.69	66.47	1509
HSA-MIR-548AV-5P	99.60	70.84	2107
HSA-MIR-548K	99.60	70.84	2107
HSA-MIR-8054	99.48	70.81	2084
HSA-MIR-6505-3P	99.34	67.39	1071
HSA-MIR-1228-3P	99.00	66.53	857
HSA-MIR-3145-3P	98.85	69.07	2031
HSA-MIR-676-5P	98.49	68.87	1492

Literature-anchored findings (GeneRIF, showing 3)

• Studies of the mouse counterpart. (PMID:12384300)
• HSPC144 was expressed and purified, and a stable fragment (residues 44-225) was identified by limited proteolysis method. (PMID:15939300)
• The 2.3A-resolution structure revealed only one 2-fold axis of rotational pseudosymmetry. A potential RNA-binding domain from human YTH-domain-containing protein 2 has the most similar 3-D fold to that of the DUF55 domain; it may be an RNA-related domain. (PMID:19237743)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	thyn1	ENSDARG00000042659
mus_musculus	Thyn1	ENSMUSG00000035443
rattus_norvegicus	Thyn1	ENSRNOG00000047053

Protein

Protein identifiers

Thymocyte nuclear protein 1 — Q9P016 (reviewed: Q9P016)

Alternative names: Thymocyte protein Thy28

All UniProt accessions (1): Q9P016

UniProt curated annotations — full annotation on UniProt →

Function. Specifically binds 5-hydroxymethylcytosine (5hmC), suggesting that it acts as a specific reader of 5hmC.

Subcellular location. Nucleus.

Post-translational modifications. Phosphorylated.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9P016-1	1	yes
Q9P016-2	2

RefSeq proteins (5): NP_001032381, NP_001032382, NP_054893, NP_954994, NP_954995 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002740	EVE_domain	Domain
IPR015947	PUA-like_sf	Homologous_superfamily
IPR047197	THYN1-like_EVE	Domain
IPR052181	5hmC_binding	Family

Pfam: PF01878

UniProt features (24 total): helix 8, strand 8, sequence conflict 2, chain 1, region of interest 1, turn 1, short sequence motif 1, compositionally biased region 1, splice variant 1

Structure

Experimental structures (PDB)

2 structures.

PDB	Method	Resolution (Å)
3EOP	X-RAY DIFFRACTION	2.3
5J3E	X-RAY DIFFRACTION	2.6

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9P016-F1	84.89	0.77

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 139 (showing top): BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_1, ZHOU_INFLAMMATORY_RESPONSE_LIVE_DN, LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN, TIEN_INTESTINE_PROBIOTICS_24HR_UP, chr11q25, NUYTTEN_EZH2_TARGETS_DN, MOREAUX_MULTIPLE_MYELOMA_BY_TACI_DN, MARSON_BOUND_BY_FOXP3_UNSTIMULATED, GOCC_NUCLEOLUS, BLALOCK_ALZHEIMERS_DISEASE_DN, THILLAINADESAN_ZNF217_TARGETS_DN, GOBERT_OLIGODENDROCYTE_DIFFERENTIATION_UP

GO Biological Process (0):

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (1): nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

752 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
THYN1	WDR76	Q9H967	766
THYN1	CD34	P28906	562
THYN1	VPS26B	Q4G0F5	517
THYN1	MYH9	P35579	483
THYN1	UHRF2	Q96PU4	472
THYN1	TRPT1	Q86TN4	472
THYN1	TRIP4	Q15650	471
THYN1	WDR75	Q8IWA0	453
THYN1	LONRF1	Q17RB8	447
THYN1	EAPP	Q56P03	437
THYN1	RNF214	Q8ND24	436
THYN1	G5EA03	G5EA03	433
THYN1	RBIS	Q8N0T1	423
THYN1	ACAD8	Q9UKU7	418
THYN1	NCAPD3	P42695	417

IntAct

19 interactions, top by confidence:

A	B	Type	Score
GPX7	GAK	psi-mi:“MI:0914”(association)	0.640
THYN1	SHPK	psi-mi:“MI:0915”(physical association)	0.590
ARIH1	SPOP	psi-mi:“MI:0914”(association)	0.530
BBS9	THYN1	psi-mi:“MI:0915”(physical association)	0.400
GOLGA2	THYN1	psi-mi:“MI:0915”(physical association)	0.370
JUN		psi-mi:“MI:0914”(association)	0.350
MAPT	MEX3A	psi-mi:“MI:0914”(association)	0.350
MAPT	C11orf98	psi-mi:“MI:0914”(association)	0.350
TAGLN	LOC392647	psi-mi:“MI:0914”(association)	0.350
	ARID1A	psi-mi:“MI:0914”(association)	0.350
MYH4	PALM3	psi-mi:“MI:0914”(association)	0.350
	HMGB3	psi-mi:“MI:0914”(association)	0.350
ARIH1	PHGDH	psi-mi:“MI:0914”(association)	0.350
ARGLU1	PIAS2	psi-mi:“MI:2364”(proximity)	0.270
NPM1	SBNO1	psi-mi:“MI:2364”(proximity)	0.270

BioGRID (37): THYN1 (Affinity Capture-MS), THYN1 (Two-hybrid), THYN1 (Affinity Capture-MS), SHPK (Affinity Capture-MS), THYN1 (Affinity Capture-MS), THYN1 (Affinity Capture-MS), THYN1 (Proximity Label-MS), THYN1 (Affinity Capture-MS), THYN1 (Affinity Capture-MS), THYN1 (Affinity Capture-MS), SHPK (Affinity Capture-MS), THYN1 (Affinity Capture-MS), THYN1 (Affinity Capture-MS), THYN1 (Co-fractionation), THYN1 (Affinity Capture-MS)

ESM2 similar proteins: C5XX79, D4A1F2, F1MF74, F1R777, F6HH45, M1JJT8, O00763, O43148, O60524, O80358, O88509, O94851, P31230, P49916, P51892, P54276, P97386, Q04499, Q08J23, Q12904, Q1MTD3, Q28E61, Q28FT4, Q28GH3, Q4R7K1, Q4V7N2, Q5U2U7, Q5ZLV4, Q60446, Q642Q1, Q6P3E0, Q6PFL8, Q7XT07, Q7ZY60, Q86U44, Q8BJ37, Q8CCP0, Q90679, Q90ZA1, Q91YJ3

Diamond homologs: O94645, Q6P3E0, Q6PFL8, Q90679, Q91YJ3, Q9P016

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	40
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1123 predictions. Top by Δscore:

Variant	Effect	Δscore
11:134248480:CTCTT:C	acceptor_gain	1.0000
11:134248482:CTT:C	acceptor_gain	1.0000
11:134248485:C:CC	acceptor_gain	1.0000
11:134249823:CTAA:C	donor_loss	1.0000
11:134249824:TAAC:T	donor_loss	1.0000
11:134249825:AACCT:A	donor_loss	1.0000
11:134249827:CCTT:C	donor_gain	1.0000
11:134249916:CGAGC:C	acceptor_gain	1.0000
11:134249920:CCTG:C	acceptor_loss	1.0000
11:134249921:C:CC	acceptor_gain	1.0000
11:134249921:CTGTC:C	acceptor_loss	1.0000
11:134249922:T:A	acceptor_loss	1.0000
11:134250339:CTGAA:C	acceptor_gain	1.0000
11:134250344:C:CC	acceptor_gain	1.0000
11:134251127:CAC:C	donor_loss	1.0000
11:134251128:A:AG	donor_loss	1.0000
11:134251129:C:A	donor_loss	1.0000
11:134251304:CTTGT:C	acceptor_gain	1.0000
11:134251305:TTGT:T	acceptor_gain	1.0000
11:134251306:TGT:T	acceptor_gain	1.0000
11:134251307:GT:G	acceptor_gain	1.0000
11:134251309:C:CC	acceptor_gain	1.0000
11:134251310:T:A	acceptor_loss	1.0000
11:134251314:A:AC	acceptor_gain	1.0000
11:134251314:A:C	acceptor_gain	1.0000
11:134251324:C:CT	acceptor_gain	1.0000
11:134251325:A:T	acceptor_gain	1.0000
11:134248483:TT:T	acceptor_gain	0.9900
11:134248483:TTCTA:T	acceptor_loss	0.9900
11:134248488:C:CT	acceptor_gain	0.9900

AlphaMissense

1489 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:134249175:A:G	W158R	0.996
11:134249175:A:T	W158R	0.996
11:134249864:G:C	S116R	0.991
11:134249864:G:T	S116R	0.991
11:134249866:T:G	S116R	0.991
11:134250298:A:G	W90R	0.991
11:134250298:A:T	W90R	0.991
11:134249173:C:A	W158C	0.990
11:134249173:C:G	W158C	0.990
11:134249916:C:G	R99P	0.989
11:134250286:G:T	R94S	0.988
11:134250327:A:G	L80P	0.987
11:134250285:C:G	R94P	0.986
11:134251172:C:A	K60N	0.986
11:134251172:C:G	K60N	0.986
11:134250296:C:A	W90C	0.985
11:134250296:C:G	W90C	0.985
11:134248907:A:G	L178P	0.982
11:134249838:C:T	G125E	0.982
11:134250281:G:C	N95K	0.981
11:134250281:G:T	N95K	0.981
11:134250341:G:C	F75L	0.981
11:134250341:G:T	F75L	0.981
11:134250343:A:G	F75L	0.981
11:134249194:G:C	S151R	0.979
11:134249194:G:T	S151R	0.979
11:134249196:T:G	S151R	0.979
11:134249847:C:T	G122D	0.979
11:134251171:A:G	S61P	0.978
11:134249844:A:T	I123N	0.977

dbSNP variants (sampled 300 via entrez): RS1000054002 (11:134254346 G>A), RS1000160445 (11:134248688 T>TA), RS1000235444 (11:134253980 C>T), RS1000388468 (11:134248228 G>A), RS1000461241 (11:134250451 T>C,G), RS1000463529 (11:134248494 A>C,G), RS1000493721 (11:134250143 T>A,C), RS1000725030 (11:134249642 T>A), RS1001492207 (11:134253893 G>A), RS1001583550 (11:134247901 C>A,T), RS1001876575 (11:134255127 T>A,C), RS1002006560 (11:134255117 A>G), RS1002052965 (11:134249725 G>A,T), RS1002116904 (11:134248951 T>C), RS1002498162 (11:134253100 C>A,T)

Disease associations

OMIM: gene MIM:613739 | 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
GCST006585_2764	Blood protein levels	6.000000e-08

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
trichostatin A	decreases expression, affects cotreatment	2
potassium chromate(VI)	affects cotreatment, decreases expression	2
Acetaminophen	decreases expression	2
Cyclosporine	decreases expression	2
aristolochic acid I	increases expression	1
dicrotophos	decreases expression	1
beauvericin	increases expression, affects cotreatment	1
bisphenol A	affects cotreatment, increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
sodium arsenite	decreases expression	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
di-n-butylphosphoric acid	affects expression	1
chromium hexavalent ion	decreases expression	1
CGP 52608	affects binding, increases reaction	1
enniatins	affects cotreatment, increases expression	1
K 7174	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	decreases expression, affects cotreatment	1
abrine	decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
jinfukang	affects cotreatment, increases expression	1
NSC 689534	affects binding, decreases expression	1
Arsenic Trioxide	increases expression	1
Cisplatin	affects cotreatment, increases expression	1
Copper	decreases expression, affects binding	1
Dexamethasone	affects cotreatment, increases expression	1
Doxorubicin	affects expression	1
Drugs, Chinese Herbal	decreases expression	1
Enzyme Inhibitors	decreases activity, increases O-linked glycosylation	1
Estradiol	decreases expression	1

Clinical trials (associated diseases)

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