TP53TG3D

Summary

TP53TG3D (TP53 target 3D, HGNC:44657) is a protein-coding gene on chromosome 16p11.2, encoding TP53-target gene 3 protein (Q9ULZ0). May play a significant role in p53/TP53-mediating signaling pathway.

Located in cytoplasm and nucleus.

Source: NCBI Gene 729264 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 3 total
• MANE Select transcript: NM_001243722

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:44657
Approved symbol	TP53TG3D
Name	TP53 target 3D
Location	16p11.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000205456
Ensembl biotype	protein_coding
Entrez	729264

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 3 nonsense_mediated_decay, 2 protein_coding, 1 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000380148, ENST00000398664, ENST00000563025, ENST00000564810, ENST00000567978, ENST00000568044, ENST00000569631

RefSeq mRNA: 1 — MANE Select: NM_001243722 NM_001243722

CCDS: CCDS58456

Canonical transcript exons

ENST00000398664 — 2 exons

Exon	Start	End
ENSE00003978229	32254891	32255928
ENSE00003978230	32253286	32253715

Expression profiles

Bgee: expression breadth ubiquitous, 126 present calls, max score 88.09.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	88.09	gold quality
right testis	UBERON:0004534	82.44	gold quality
testis	UBERON:0000473	82.36	gold quality
left testis	UBERON:0004533	82.12	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	76.87	gold quality
lower esophagus mucosa	UBERON:0035834	75.73	gold quality
cerebellum	UBERON:0002037	66.31	gold quality
cerebellar cortex	UBERON:0002129	66.22	gold quality
cerebellar hemisphere	UBERON:0002245	66.21	gold quality
right hemisphere of cerebellum	UBERON:0014890	65.38	gold quality
stromal cell of endometrium	CL:0002255	64.59	gold quality
placenta	UBERON:0001987	64.50	gold quality
monocyte	CL:0000576	64.47	gold quality
leukocyte	CL:0000738	63.71	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	61.97	gold quality
Brodmann (1909) area 9	UBERON:0013540	60.60	gold quality
endometrium	UBERON:0001295	59.78	gold quality
esophagus mucosa	UBERON:0002469	59.64	gold quality
cortical plate	UBERON:0005343	59.60	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	59.30	gold quality
right frontal lobe	UBERON:0002810	58.99	gold quality
right atrium auricular region	UBERON:0006631	58.49	gold quality
descending thoracic aorta	UBERON:0002345	58.31	gold quality
superior frontal gyrus	UBERON:0002661	58.02	gold quality
granulocyte	CL:0000094	57.83	gold quality
heart left ventricle	UBERON:0002084	57.56	gold quality
ganglionic eminence	UBERON:0004023	57.27	gold quality
islet of Langerhans	UBERON:0000006	56.89	gold quality
esophagus	UBERON:0001043	56.80	gold quality
heart	UBERON:0000948	56.31	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.53

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

70 targeting TP53TG3D, 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-3646	100.00	73.56	5283
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-551B-5P	99.96	71.28	3493
HSA-MIR-539-5P	99.93	70.30	2855
HSA-MIR-627-3P	99.90	71.42	3316
HSA-MIR-380-3P	99.89	70.18	1978
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-12119	99.87	68.35	1653
HSA-MIR-6875-3P	99.82	70.26	2983
HSA-MIR-3180-5P	99.82	69.12	2422
HSA-MIR-8080	99.82	67.52	1342
HSA-MIR-548F-5P	99.78	71.02	3093
HSA-MIR-4524A-3P	99.72	66.85	2406
HSA-MIR-3714	99.71	70.74	2671
HSA-MIR-4690-5P	99.65	66.24	813
HSA-MIR-561-3P	99.64	70.90	3647
HSA-MIR-6126	99.62	68.09	996
HSA-MIR-548AV-5P	99.60	70.84	2107
HSA-MIR-548K	99.60	70.84	2107
HSA-MIR-4649-3P	99.56	66.90	1783
HSA-MIR-1252-3P	99.55	67.71	2862
HSA-MIR-17-3P	99.55	66.77	1311
HSA-MIR-7159-5P	99.53	72.12	2472
HSA-MIR-8054	99.48	70.81	2084

Cross-species orthologs

0 orthologs

Paralogs (7): TP53TG3 (ENSG00000183632), TP53TG3C (ENSG00000205457), TP53TG3B (ENSG00000261509), (ENSG00000274175), TP53TG3E (ENSG00000275034), (ENSG00000275869), TP53TG3F (ENSG00000278848)

Protein

Protein identifiers

TP53-target gene 3 protein — Q9ULZ0 (reviewed: Q9ULZ0)

Alternative names: TP53-inducible gene 3 protein

All UniProt accessions (3): Q9ULZ0, A0A1Y8EMM2, H3BT92

UniProt curated annotations — full annotation on UniProt →

Function. May play a significant role in p53/TP53-mediating signaling pathway.

Subcellular location. Cytoplasm. Nucleus.

Tissue specificity. Strongly expressed in testis. Weakly expressed in heart, placenta and skeletal muscle.

Induction. By p53/TP53.

Miscellaneous. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

Isoforms (3)

UniProt ID	Names	Canonical?
Q9ULZ0-2	2, TP53TG3a	yes
Q9ULZ0-1	1, TP53TG3b
Q9ULZ0-3	3

RefSeq proteins (1): NP_001230651* (*=MANE)

Domains & families (InterPro)

UniProt features (6 total): splice variant 3, chain 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9ULZ0-F1	40.37	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 19 (showing top): chr16p11, MIR3646, MIR548AW, MIR551B_5P, MIR561_3P, MIR3065_5P, MIR539_5P, MIR4291, MIR1252_3P, MIR4801, MIR4731_3P, MIR509_5P, MIR509_3_5P, MIR4766_3P, MIR17_3P

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (2): nucleus (GO:0005634), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
intracellular membrane-bounded organelle	1
intracellular anatomical structure	1
cellular anatomical structure	1

Protein interactions and networks

STRING

268 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TP53TG3D	TP53I11	O14683	400
TP53TG3D	PGBD2	Q6P3X8	398
TP53TG3D	GLYATL3	Q5SZD4	393
TP53TG3D	ZNF672	Q499Z4	370
TP53TG3D	TP53TG5	Q9Y2B4	352
TP53TG3D	FAM174A	Q8TBP5	351
TP53TG3D	ZNF595	Q8IYB9	348
TP53TG3D	ZNF280A	P59817	325
TP53TG3D	HEATR5B	Q9P2D3	324
TP53TG3D	VSIG10	Q8N0Z9	323
TP53TG3D	FAM72B	Q86X60	314
TP53TG3D	DYDC2	Q96IM9	310
TP53TG3D	SLC6A8	P48029	306
TP53TG3D	TP53I13	Q8NBR0	305
TP53TG3D	SMIM3	Q9BZL3	297

IntAct

1 interactions, top by confidence:

BioGRID (5): TP53TG3C (Negative Genetic), TP53TG3C (Negative Genetic), TP53TG3B (Negative Genetic), TP53TG3 (Positive Genetic), TP53TG3 (Affinity Capture-RNA)

ESM2 similar proteins: A0A1B0GUT2, A0A3Q1LFG5, A1L4Q6, A2RUQ5, A8MQB3, A8MU10, B1ANY3, C0HM98, H3BQW9, J3KSC0, P0C092, P0DMU3, P0DPA3, P24026, P59020, P59021, P59052, P87743, Q06250, Q0IIN9, Q0VFX4, Q14695, Q4R3X9, Q4VX62, Q52M75, Q5SR53, Q6ZUF6, Q6ZWC4, Q71F78, Q7Z4H9, Q8JMY5, Q8JMZ5, Q8JN06, Q8N2C9, Q8N2X6, Q8N3U1, Q8N9X3, Q8NAA6, Q8NBC4, Q8NDY4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

364 predictions. Top by Δscore:

Variant	Effect	Δscore
16:32254562:C:G	donor_gain	0.9900
16:32254556:A:T	donor_gain	0.9700
16:32254581:G:GT	donor_gain	0.9700
16:32254555:G:GT	donor_gain	0.9500
16:32254525:G:GT	donor_gain	0.9300
16:32253463:TTG:T	donor_gain	0.9200
16:32253711:TCAAG:T	donor_loss	0.9200
16:32253712:CAAGG:C	donor_loss	0.9200
16:32253713:AAGGT:A	donor_loss	0.9200
16:32253714:AG:A	donor_loss	0.9200
16:32253715:G:GT	donor_loss	0.9200
16:32253716:GTA:G	donor_loss	0.9200
16:32253717:T:G	donor_loss	0.9200
16:32253570:C:G	donor_gain	0.9100
16:32254005:G:GT	donor_gain	0.9100
16:32254647:GGTC:G	donor_gain	0.9100
16:32254886:TTAA:T	acceptor_gain	0.8900
16:32254887:TAA:T	acceptor_gain	0.8900
16:32254888:AAG:A	acceptor_gain	0.8900
16:32254889:A:T	acceptor_gain	0.8900
16:32253678:C:A	donor_gain	0.8800
16:32253710:GTCAA:G	donor_loss	0.8800
16:32254890:G:T	acceptor_gain	0.8800
16:32254550:C:CG	donor_gain	0.8700
16:32254100:T:TA	donor_gain	0.8600
16:32254101:A:AA	donor_gain	0.8600
16:32253718:A:C	donor_loss	0.8500
16:32254730:T:TA	donor_gain	0.8400
16:32254731:A:AA	donor_gain	0.8400
16:32253708:TTGTC:T	donor_gain	0.8300

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1003539675 (16:32251911 C>T), RS1003739139 (16:32252761 A>G,T), RS1004757340 (16:32252997 G>T), RS1004956860 (16:32254022 G>A), RS1011003189 (16:32251845 A>G), RS1011097805 (16:32251577 A>G,T), RS1012630492 (16:32252905 C>T), RS1014757515 (16:32253003 G>A,C), RS1014994060 (16:32254054 C>A,T), RS1021142008 (16:32251582 T>C), RS1022685947 (16:32255104 A>G), RS1023140448 (16:32255787 T>C), RS1027747132 (16:32252966 G>A), RS1028487353 (16:32251548 A>G), RS1028912832 (16:32254128 A>G)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

Clinical trials (associated diseases)

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