TRNP1

Summary

TRNP1 (TMF1 regulated nuclear protein 1, HGNC:34348) is a protein-coding gene on chromosome 1p36.11, encoding TMF-regulated nuclear protein 1 (Q6NT89). DNA-binding factor that regulates the expression of a subset of genes and plays a key role in tangential, radial, and lateral expansion of the brain neocortex.

Predicted to enable DNA binding activity. Predicted to be involved in several processes, including cerebellar cortex morphogenesis; neural precursor cell proliferation; and regulation of cell population proliferation. Predicted to be located in euchromatin. Predicted to be active in nucleus.

Source: NCBI Gene 388610 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 53 total
• MANE Select transcript: NM_001013642

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:34348
Approved symbol	TRNP1
Name	TMF1 regulated nuclear protein 1
Location	1p36.11
Locus type	gene with protein product
Status	Approved
Aliases	TRNP
Ensembl gene	ENSG00000253368
Ensembl biotype	protein_coding
OMIM	616824
Entrez	388610

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000522111, ENST00000531285

RefSeq mRNA: 1 — MANE Select: NM_001013642 NM_001013642

CCDS: CCDS41289

Canonical transcript exons

ENST00000522111 — 2 exons

Exon	Start	End
ENSE00002093924	26999847	27000886
ENSE00002107275	26993692	26994612

Expression profiles

Bgee: expression breadth ubiquitous, 241 present calls, max score 97.77.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 3.9237 / max 144.1127, expressed in 1003 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
1677	9.6762	1323
1679	2.8580	858
1678	0.5385	336
1681	0.2738	118
1680	0.2535	110
1676	0.1526	62

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cardiac muscle of right atrium	UBERON:0003379	97.77	gold quality
lateral nuclear group of thalamus	UBERON:0002736	97.14	gold quality
pharyngeal mucosa	UBERON:0000355	96.16	gold quality
esophagus mucosa	UBERON:0002469	94.52	gold quality
lower esophagus mucosa	UBERON:0035834	94.32	gold quality
left ventricle myocardium	UBERON:0006566	93.97	gold quality
nasal cavity epithelium	UBERON:0005384	93.61	gold quality
epithelial cell of pancreas	CL:0000083	93.33	silver quality
body of stomach	UBERON:0001161	93.15	gold quality
pylorus	UBERON:0001166	92.91	gold quality
esophagus squamous epithelium	UBERON:0006920	92.77	gold quality
palpebral conjunctiva	UBERON:0001812	92.59	gold quality
pancreatic ductal cell	CL:0002079	92.53	gold quality
islet of Langerhans	UBERON:0000006	92.30	gold quality
stomach	UBERON:0000945	92.09	gold quality
decidua	UBERON:0002450	92.06	gold quality
esophagus	UBERON:0001043	91.52	gold quality
substantia nigra pars compacta	UBERON:0001965	90.96	gold quality
cardia of stomach	UBERON:0001162	90.94	gold quality
Brodmann (1909) area 23	UBERON:0013554	90.75	gold quality
dorsal root ganglion	UBERON:0000044	90.56	gold quality
Brodmann (1909) area 9	UBERON:0013540	90.52	gold quality
germinal epithelium of ovary	UBERON:0001304	90.47	gold quality
oral cavity	UBERON:0000167	90.45	gold quality
fundus of stomach	UBERON:0001160	90.43	gold quality
cardiac atrium	UBERON:0002081	90.03	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	90.02	gold quality
substantia nigra pars reticulata	UBERON:0001966	89.83	gold quality
right atrium auricular region	UBERON:0006631	89.72	gold quality
right frontal lobe	UBERON:0002810	89.70	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-GEOD-137537	yes	1898.53
E-MTAB-11121	yes	1065.88
E-ANND-3	no	2.65

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

59 targeting TRNP1, 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-5193	100.00	67.26	1744
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-511-3P	99.99	68.85	1467
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-1236-3P	99.94	68.04	1695
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-515-5P	99.92	69.82	2343
HSA-MIR-519E-5P	99.92	69.62	2358
HSA-MIR-4731-5P	99.89	67.23	2537
HSA-MIR-12119	99.87	68.35	1653
HSA-MIR-3151-5P	99.86	63.83	1069
HSA-MIR-4447	99.85	67.81	2900
HSA-MIR-4668-5P	99.79	70.58	3782
HSA-MIR-6794-5P	99.76	66.38	1048
HSA-MIR-1200	99.71	70.42	1838
HSA-MIR-378G	99.71	64.90	1106
HSA-MIR-3714	99.71	70.74	2671
HSA-MIR-4716-3P	99.69	66.73	1022
HSA-MIR-4527	99.66	67.43	714
HSA-MIR-378A-5P	99.65	66.33	1311
HSA-MIR-6503-5P	99.62	66.96	597
HSA-MIR-4472	99.56	66.08	1478
HSA-MIR-5584-5P	99.49	68.22	2814
HSA-MIR-3140-5P	99.39	69.04	1136
HSA-MIR-940	99.37	66.14	2064

Literature-anchored findings (GeneRIF, showing 1)

• TRNP1 expression levels exhibit regional differences in the cerebral cortex of human fetuses, anticipating radial or tangential expansion. (PMID:23622239)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	si:ch211-160f23.7	ENSDARG00000100722
mus_musculus	Trnp1	ENSMUSG00000056596
rattus_norvegicus	Trnp1	ENSRNOG00000055936

Protein

Protein identifiers

TMF-regulated nuclear protein 1 — Q6NT89 (reviewed: Q6NT89)

All UniProt accessions (2): H0YES3, Q6NT89

UniProt curated annotations — full annotation on UniProt →

Function. DNA-binding factor that regulates the expression of a subset of genes and plays a key role in tangential, radial, and lateral expansion of the brain neocortex. Regulates neural stem cells proliferation and the production of intermediate neural progenitors and basal radial glial cells affecting the process of cerebral cortex gyrification. May control the proliferation rate of cells by regulating their progression through key cell-cycle transition points.

Subunit / interactions. Interacts with TMF1; may regulate TRNP1 proteasomal degradation.

Subcellular location. Nucleus.

Post-translational modifications. Ubiquitinated, leading to its degradation by the proteasome.

RefSeq proteins (1): NP_001013664* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR040266	TRNP1	Family

UniProt features (5 total): region of interest 2, chain 1, compositionally biased region 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6NT89-F1	70.32	0.31

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 88 (showing top): GOBP_HINDBRAIN_DEVELOPMENT, GOBP_METENCEPHALON_DEVELOPMENT, GOBP_CEREBELLAR_CORTEX_MORPHOGENESIS, LINDGREN_BLADDER_CANCER_CLUSTER_3_DN, BRUECKNER_TARGETS_OF_MIRLET7A3_DN, GOBP_NEURAL_PRECURSOR_CELL_PROLIFERATION, GOBP_CEREBELLAR_CORTEX_DEVELOPMENT, WANG_LMO4_TARGETS_DN, GOBP_REGULATION_OF_CELL_CYCLE, GOBP_HEAD_DEVELOPMENT, GOBP_HINDBRAIN_MORPHOGENESIS, CTCTATG_MIR368, GOCC_EUCHROMATIN, DODD_NASOPHARYNGEAL_CARCINOMA_DN, chr1p36

GO Biological Process (5): cerebellar cortex morphogenesis (GO:0021696), regulation of cell population proliferation (GO:0042127), regulation of cell cycle (GO:0051726), neural precursor cell proliferation (GO:0061351), nervous system development (GO:0007399)

GO Molecular Function (1): DNA binding (GO:0003677)

GO Cellular Component (2): euchromatin (GO:0000791), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cell population proliferation	2
regulation of cellular process	2
anatomical structure morphogenesis	1
cerebellum morphogenesis	1
cerebellar cortex development	1
cell cycle	1
system development	1
nucleic acid binding	1
chromatin	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

466 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TRNP1	ARHGAP11B	Q3KRB8	630
TRNP1	TMEM14B	Q9NUH8	473
TRNP1	UBTF	P17480	451
TRNP1	PLEKHG6	Q3KR16	448
TRNP1	SEMG1	P04279	415
TRNP1	HAPLN1	P10915	407
TRNP1	PAX6	P26367	388
TRNP1	LUM	P51884	378
TRNP1	RCOR2	Q8IZ40	363
TRNP1	EOMES	O95936	363
TRNP1	C6orf118	Q5T5N4	357
TRNP1	DNPH1	O43598	339
TRNP1	SMARCC2	Q8TAQ2	337
TRNP1	PRAP1	Q96NZ9	335
TRNP1	ADGRG1	Q9Y653	333

IntAct

3 interactions, top by confidence:

A	B	Type	Score
P		psi-mi:“MI:0914”(association)	0.350
SNAP29	SNAP23	psi-mi:“MI:0914”(association)	0.350

BioGRID (5): TRNP1 (Affinity Capture-RNA), TRNP1 (Affinity Capture-MS), TRNP1 (Affinity Capture-RNA), TRNP1 (Affinity Capture-MS), TRNP1 (Affinity Capture-RNA)

ESM2 similar proteins: A0A0U1RRK4, A0A1W2PPE3, A0A2R8Y2Y2, A0A494C0N9, A0A494C0Y3, A6NC62, A6NHQ4, A8MTW9, B2RU40, C9JH25, C9JUS6, C9JVW0, D4A9R4, F8WCM5, H3BQW9, I3L1E1, M0QZC1, O75474, O75638, P0C7X2, P0DPE3, P19601, P19998, P70339, Q1HCM0, Q32M26, Q3UM83, Q5BLP8, Q5FWE3, Q5RCL0, Q5U2P6, Q6NT89, Q6NUJ2, Q6NZ36, Q6PE13, Q7RTU4, Q7RTU5, Q7TNS8, Q80ZG6, Q80ZI1

Diamond homologs: Q6NT89, Q80ZI1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	49
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

1391 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:26994187:T:C	F134S	0.994
1:26994154:T:C	L123P	0.991
1:26994157:A:T	E124V	0.991
1:26994195:G:C	A137P	0.991
1:26994115:T:C	L110P	0.990
1:26994175:T:C	L130P	0.990
1:26994199:A:T	E138V	0.990
1:26994102:G:C	A106P	0.985
1:26994202:T:C	L139P	0.983
1:26994186:T:C	F134L	0.981
1:26994188:C:A	F134L	0.981
1:26994188:C:G	F134L	0.981
1:26994377:G:C	W197C	0.976
1:26994377:G:T	W197C	0.976
1:26994196:C:A	A137D	0.974
1:26994109:G:C	R108P	0.972
1:26994187:T:G	F134C	0.971
1:26994366:T:C	C194R	0.971
1:26994156:G:A	E124K	0.970
1:26994127:A:T	E114V	0.969
1:26994158:G:C	E124D	0.969
1:26994158:G:T	E124D	0.969
1:26994198:G:A	E138K	0.968
1:26994177:C:G	H131D	0.967
1:26994349:C:A	A188E	0.967
1:26994258:G:C	A158P	0.964
1:26994090:G:A	E102K	0.963
1:26994163:G:C	R126P	0.963
1:26994367:G:A	C194Y	0.962
1:26994375:T:A	W197R	0.962

dbSNP variants (sampled 300 via entrez): RS1000155928 (1:26996911 C>T), RS1000838370 (1:26994837 C>T), RS1000989524 (1:27001246 A>T), RS1001057569 (1:26993781 C>G,T), RS1001065922 (1:27000949 GACA>G), RS1001092699 (1:26997991 A>G), RS1001426351 (1:26996460 G>T), RS1002124458 (1:26993942 G>C), RS1002860042 (1:26992221 G>A), RS1003344973 (1:27000219 A>G), RS1003431975 (1:26993066 G>C), RS1003574350 (1:26992564 G>A), RS1003631347 (1:26996980 TAAC>T), RS1003958276 (1:26997316 A>G), RS1004056870 (1:26999877 A>G)

Disease associations

OMIM: gene MIM:616824 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST90002398_46	Neutrophil count	2.000000e-12
GCST90002407_392	White blood cell count	3.000000e-10

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004833	neutrophil count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression	7
Benzo(a)pyrene	affects methylation, increases expression	5
trichostatin A	increases expression, affects cotreatment	3
entinostat	affects cotreatment, increases expression	2
belinostat	increases expression, affects cotreatment	2
Vorinostat	affects cotreatment, increases expression	2
Panobinostat	increases expression, affects cotreatment	2
Acetaminophen	decreases expression, increases expression	2
Arsenic	affects methylation, increases abundance, increases expression	2
Estradiol	affects expression, affects cotreatment, decreases expression	2
Lipopolysaccharides	affects cotreatment, decreases expression, affects expression, affects response to substance	2
Phenylmercuric Acetate	affects cotreatment, increases expression	2
Tetrachlorodibenzodioxin	affects expression, increases expression	2
Tretinoin	decreases expression, increases expression	2
bisphenol A	decreases methylation	1
sodium arsenate	increases abundance, increases expression	1
sodium arsenite	increases expression	1
benzo(e)pyrene	decreases methylation	1
S-(1,2-dichlorovinyl)cysteine	affects cotreatment, decreases expression	1
polyhexamethyleneguanidine	affects expression	1
K 7174	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
abrine	increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
licochalcone B	increases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Zoledronic Acid	decreases expression	1
Leflunomide	increases expression	1
Air Pollutants	decreases expression, increases abundance	1
Cadmium	increases abundance, increases expression	1

Clinical trials (associated diseases)

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