MYCT1

Summary

MYCT1 (MYC target 1, HGNC:23172) is a protein-coding gene on chromosome 6q25.2, encoding Myc target protein 1 (Q8N699). May regulate certain MYC target genes, MYC seems to be a direct upstream transcriptional activator.

Predicted to act upstream of or within hematopoietic stem cell homeostasis. Located in nuclear body.

Source: NCBI Gene 80177 — RefSeq curated summary.

At a glance

• GWAS associations: 11
• Clinical variants (ClinVar): 12 total
• MANE Select transcript: NM_025107

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23172
Approved symbol	MYCT1
Name	MYC target 1
Location	6q25.2
Locus type	gene with protein product
Status	Approved
Aliases	MTLC, FLJ21269
Ensembl gene	ENSG00000120279
Ensembl biotype	protein_coding
OMIM	616805
Entrez	80177

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000367245, ENST00000529453, ENST00000532295

RefSeq mRNA: 4 — MANE Select: NM_025107 NM_001371624, NM_001371625, NM_001371626, NM_025107

CCDS: CCDS5239

Canonical transcript exons

ENST00000367245 — 2 exons

Exon	Start	End
ENSE00001443922	152721742	152724569
ENSE00002192914	152697897	152698098

Expression profiles

Bgee: expression breadth ubiquitous, 242 present calls, max score 88.84.

FANTOM5 (CAGE): breadth broad, TPM avg 15.1784 / max 491.7479, expressed in 554 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
70648	10.3692	495
70647	4.8092	470

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
lower lobe of lung	UBERON:0008949	88.84	gold quality
subcutaneous adipose tissue	UBERON:0002190	88.69	gold quality
adipose tissue	UBERON:0001013	88.65	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	88.64	gold quality
omental fat pad	UBERON:0010414	88.32	gold quality
adipose tissue of abdominal region	UBERON:0007808	88.31	gold quality
peritoneum	UBERON:0002358	88.23	gold quality
connective tissue	UBERON:0002384	87.90	gold quality
bronchial epithelial cell	CL:0002328	87.21	gold quality
mucosa of paranasal sinus	UBERON:0005030	85.98	gold quality
spleen	UBERON:0002106	85.91	gold quality
calcaneal tendon	UBERON:0003701	85.83	gold quality
buccal mucosa cell	CL:0002336	85.65	gold quality
colonic epithelium	UBERON:0000397	85.57	gold quality
upper lobe of lung	UBERON:0008948	85.01	gold quality
superficial temporal artery	UBERON:0001614	84.92	gold quality
upper lobe of left lung	UBERON:0008952	84.69	gold quality
apex of heart	UBERON:0002098	84.47	gold quality
right lung	UBERON:0002167	84.47	gold quality
tendon of biceps brachii	UBERON:0008188	84.05	gold quality
tendon	UBERON:0000043	83.56	gold quality
heart left ventricle	UBERON:0002084	82.81	gold quality
cardiac ventricle	UBERON:0002082	82.73	gold quality
gall bladder	UBERON:0002110	82.59	gold quality
biceps brachii	UBERON:0001507	82.48	gold quality
parietal pleura	UBERON:0002400	82.48	gold quality
right lobe of thyroid gland	UBERON:0001119	81.78	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	81.70	gold quality
thoracic mammary gland	UBERON:0005200	81.56	gold quality
heart right ventricle	UBERON:0002080	81.55	gold quality

Single-cell (SCXA)

Detected in 13 experiment(s), a significant marker in 12.

Experiment	Marker?	Max mean expression
E-GEOD-83139	yes	599.76
E-ENAD-27	yes	446.10
E-GEOD-76312	yes	375.42
E-MTAB-10553	yes	48.71
E-HCAD-11	yes	40.72
E-HCAD-10	yes	36.12
E-MTAB-6701	yes	16.38
E-HCAD-9	yes	15.40
E-GEOD-135922	yes	11.42
E-MTAB-5061	yes	6.44
E-GEOD-130148	yes	4.09
E-MTAB-6678	no	3.83
E-ANND-3	no	0.00

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

6 targets.

Target	Regulation
BAX	Activation
BCL2	Repression
CCND1	Repression
CCND2	Repression
CCNE1	Repression
CCNE2	Repression

Upstream regulators (CollecTRI, top): MAX, MYC

miRNA regulators (miRDB)

137 targeting MYCT1, 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-3134	100.00	66.43	777
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-3925-3P	100.00	69.95	1237
HSA-MIR-450A-1-3P	100.00	69.33	1837
HSA-MIR-4682	100.00	68.89	1258
HSA-MIR-3185	99.99	68.12	1959
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-539-3P	99.98	70.74	1616
HSA-MIR-485-3P	99.98	70.68	1585
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-1250-3P	99.96	70.04	4038
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-3658	99.96	73.87	4379
HSA-MIR-23A-3P	99.95	74.24	3163
HSA-MIR-23B-3P	99.95	74.24	3163
HSA-MIR-23C	99.95	73.92	3192
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-1236-3P	99.94	68.04	1695

Literature-anchored findings (GeneRIF, showing 16)

• MTLC was down-regulated in the majority of gastric cancer tissues and could promote apoptosis of GC cell lines, which suggests that MTLC may play an important role in the carcinogenesis of gastric carcinoma. (PMID:14562369)
• results suggest MYCT1 transcription can be activated downstream of RUNX1-ETO as well as MYC, contributing to key aspects of the leukaemic phenotypes these oncoproteins promote (PMID:21799513)
• MYCT1-TV, a novel MYCT1 transcript, is regulated by c-Myc and down-regulation of MYCT1-TV/MYCT1 could contribute to LSCC development and function (PMID:21998677)
• hypermethylation contributed to the transcriptional down-regulation of MYCT1 and could inhibit cancer cell differentiation in laryngeal squamous cell cancer. (PMID:22672838)
• Data indicate 3 variants in 3 novel genes myc target 1 protein (MYCT1), caspase recruitment domain family member 8 (CARD8) and zinc finger protein 543 (ZNF543), associated with familial IgA nephropathy (IgAN). (PMID:26095808)
• Overexpression of MYCT1, decreased cell viability under serum deprivation and increased tumour cell migration ability. (PMID:26710964)
• this study has provided the theoretical basis for the further discussion of the effect and mechanism of action of MTLC in the occurrence of laryngeal cancer. (PMID:27072211)
• YY1 promotes proliferation and migration with suppression of apoptosis via directly inhibiting MYCT1 in laryngeal cancer cells, suggesting that YY1 is a useful target as a potential oncogene in laryngeal cancer development and progression. (PMID:28485541)
• miR-632 was upregulated and MYCT1 was downregulated in HCC. High miR-632 or low MYCT1 expression was shown as a predictor for poor overall survival of HCC patients. The study also found miR-632 was able to regulate HCC cell growth and invasion through targeting the expression of MYCT1. (PMID:30982352)
• MYCT1 may synergistically interact with MAX as a co-transcription factor or a component of MAX transcriptional complex, to transcriptionally regulate the expression of miR-181a, which, in turn, decreases NPM1 expression at post-transcriptional levels, leading to enhanced apoptosis in laryngeal cancer cells (PMID:31152622)
• MYCT1 inhibits the EMT and migration of laryngeal cancer cells via the SP1/miR-629-3p/ESRP2 pathway. (PMID:32659265)
• Dual role of endothelial Myct1 in tumor angiogenesis and tumor immunity. (PMID:33658356)
• Nitrosative stress induces downregulation of ribosomal protein genes via MYCT1 in vascular smooth muscle cells. (PMID:34604957)
• MYCT1 in cancer development: Gene structure, regulation, and biological implications for diagnosis and treatment. (PMID:37499454)
• MYCT-1 Gene Expression in Patients with Gastric Cancer: an Ex Vivo Study. (PMID:38112991)
• MYCT1 inhibits hematopoiesis in diffuse large B-cell lymphoma by suppressing RUNX1 transcription. (PMID:38172714)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	myct1a	ENSDARG00000056125
danio_rerio	myct1b	ENSDARG00000088546
mus_musculus	Myct1	ENSMUSG00000046916
rattus_norvegicus	Myct1	ENSRNOG00000018858

Protein

Protein identifiers

Myc target protein 1 — Q8N699 (reviewed: Q8N699)

Alternative names: Myc target in myeloid cells protein 1

All UniProt accessions (3): E9PQ55, Q8N699, H0YDV5

UniProt curated annotations — full annotation on UniProt →

Function. May regulate certain MYC target genes, MYC seems to be a direct upstream transcriptional activator. Does not seem to significantly affect growth cell capacity. Overexpression seems to mediate many of the known phenotypic features associated with MYC, including promotion of apoptosis, alteration of morphology, enhancement of anchorage-independent growth, tumorigenic conversion, promotion of genomic instability, and inhibition of hematopoietic differentiation.

Subcellular location. Nucleus.

Tissue specificity. Down-regulated in gastric cancer tissues.

Similarity. Belongs to the MYCT1 family.

RefSeq proteins (4): NP_001358553, NP_001358554, NP_001358555, NP_079383* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR029180	Myc_target_1	Family

Pfam: PF15179

UniProt features (9 total): modified residue 4, sequence variant 2, chain 1, short sequence motif 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N699-F1	60.91	0.06

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (4): 135, 138, 141, 149

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 154 (showing top): GCANCTGNY_MYOD_Q6, EVI1_05, chr6q25, SOX9_B1, GATA6_01, GRE_C, TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_10D_UP, CORRE_MULTIPLE_MYELOMA_UP, TATA_C, RYTTCCTG_ETS2_B, GOBP_MULTICELLULAR_ORGANISMAL_LEVEL_HOMEOSTASIS, SENESE_HDAC1_TARGETS_UP, JAATINEN_HEMATOPOIETIC_STEM_CELL_UP, CUI_TCF21_TARGETS_2_DN, GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_TURQUOISE_UP

GO Biological Process (1): hematopoietic stem cell homeostasis (GO:0061484)

GO Molecular Function (0):

GO Cellular Component (4): nucleoplasm (GO:0005654), nuclear body (GO:0016604), nucleus (GO:0005634), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
homeostasis of number of cells	1
nuclear lumen	1
nucleoplasm	1
intracellular membraneless organelle	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

652 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
MYCT1	ADGRL4	Q9HBW9	462
MYCT1	CKAP4	Q07065	432
MYCT1	DDX42	Q86XP3	425
MYCT1	APPL1	Q9UKG1	372
MYCT1	GPATCH1	Q9BRR8	369
MYCT1	GLG1	Q92896	366
MYCT1	EMCN	Q9ULC0	361
MYCT1	TINAGL1	Q9GZM7	355
MYCT1	APPL2	Q8NEU8	348
MYCT1	DHX15	O43143	347
MYCT1	PTDSS1	P48651	324
MYCT1	STX6	O43752	317
MYCT1	C1orf198	Q9H425	316
MYCT1	ZNF543	Q08ER8	311
MYCT1	ENGASE	Q8NFI3	310

IntAct

11 interactions, top by confidence:

A	B	Type	Score
ITCH	MYCT1	psi-mi:“MI:0407”(direct interaction)	0.440
NEDD4	MYCT1	psi-mi:“MI:0407”(direct interaction)	0.440
MYCT1	PCNA	psi-mi:“MI:0915”(physical association)	0.370
ANG	DDX39A	psi-mi:“MI:0914”(association)	0.350
MYCT1	SPTLC2	psi-mi:“MI:0914”(association)	0.350
TRIM63	MYCT1	psi-mi:“MI:0915”(physical association)	0.000
TRIM55	MYCT1	psi-mi:“MI:0915”(physical association)	0.000
MYCT1	ftsK	psi-mi:“MI:0915”(physical association)	0.000
tcaA1	MYCT1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (16): MYCT1 (Two-hybrid), MYCT1 (Two-hybrid), SPTLC2 (Affinity Capture-MS), NDFIP1 (Affinity Capture-MS), DDR1 (Affinity Capture-MS), SCAP (Affinity Capture-MS), CIB1 (Affinity Capture-MS), SCGB1D2 (Affinity Capture-MS), MYCT1 (Protein-peptide), MYCT1 (Protein-peptide), MYCT1 (Protein-peptide), MYCT1 (Affinity Capture-MS), MYCT1 (Affinity Capture-MS), MYCT1 (Affinity Capture-Western), MARCH1 (Affinity Capture-Western)

ESM2 similar proteins: A0A482ARP7, A0A482ATU4, A7TI28, A9Q1J7, C4QVX6, F5HGQ8, O43009, O59776, O94400, P16200, P16208, P27272, P27908, P28979, P34530, P34664, P40688, P41698, P41884, P53891, P53895, P67908, P67909, P87119, Q00102, Q03345, Q04461, Q08D18, Q5I150, Q5SNQ9, Q5UQ56, Q66262, Q69505, Q69559, Q6F6K2, Q77MT3, Q84W40, Q8L9T5, Q8N699, Q8NIP8

Diamond homologs: Q08D18, Q5SNQ9, Q8N699, Q8R411

SIGNOR signaling

11 interactions.

A	Effect	B	Mechanism
MYCT1	down-regulates	Proliferation
MYCT1	up-regulates	Apoptosis
MYCT1	“down-regulates quantity by repression”	CCND1	“transcriptional regulation”
MYCT1	“down-regulates quantity by repression”	CCND2	“transcriptional regulation”
MYCT1	“down-regulates quantity by repression”	CCNE1	“transcriptional regulation”
MYCT1	“down-regulates quantity by repression”	CCNE2	“transcriptional regulation”
MYCT1	“up-regulates quantity by expression”	BAX	“transcriptional regulation”
MYCT1	“down-regulates quantity by repression”	BCL2	“transcriptional regulation”
MYCT1	“up-regulates activity”	CASP3
MYCT1	“up-regulates activity”	CASP9
MYC	“up-regulates quantity by expression”	MYCT1	“transcriptional regulation”

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	6
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

429 predictions. Top by Δscore:

Variant	Effect	Δscore
6:152721737:TTCA:T	acceptor_loss	1.0000
6:152721738:TCAGA:T	acceptor_loss	1.0000
6:152721739:CA:C	acceptor_loss	1.0000
6:152721740:A:AG	acceptor_gain	1.0000
6:152721740:A:C	acceptor_loss	1.0000
6:152721740:AGAG:A	acceptor_gain	1.0000
6:152721741:G:GA	acceptor_gain	1.0000
6:152721741:GA:G	acceptor_gain	1.0000
6:152721741:GAGG:G	acceptor_gain	1.0000
6:152721741:GAGGA:G	acceptor_gain	1.0000
6:152706039:T:TA	donor_gain	0.9800
6:152706040:A:AA	donor_gain	0.9800
6:152698095:TGGG:T	donor_loss	0.9700
6:152698098:GGTAA:G	donor_loss	0.9700
6:152698099:G:GA	donor_loss	0.9700
6:152698100:T:A	donor_loss	0.9700
6:152713994:T:TA	donor_gain	0.9700
6:152713995:A:AA	donor_gain	0.9700
6:152698097:GG:G	donor_gain	0.9600
6:152698098:GG:G	donor_gain	0.9600
6:152698099:G:GG	donor_gain	0.9600
6:152721734:T:TA	acceptor_gain	0.9600
6:152721738:TCAG:T	acceptor_gain	0.9600
6:152721739:CAG:C	acceptor_gain	0.9600
6:152721740:AGA:A	acceptor_gain	0.9600
6:152721741:GAG:G	acceptor_gain	0.9600
6:152698096:GGG:G	donor_gain	0.9500
6:152698097:GGG:G	donor_gain	0.9500
6:152705974:GATT:G	donor_gain	0.9500
6:152713985:GCCTT:G	acceptor_gain	0.9500

AlphaMissense

1529 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
6:152722044:T:C	F167L	0.998
6:152722046:C:A	F167L	0.998
6:152722046:C:G	F167L	0.998
6:152721966:A:C	S141R	0.995
6:152721968:T:A	S141R	0.995
6:152721968:T:G	S141R	0.995
6:152722039:C:T	S165F	0.994
6:152721957:A:C	S138R	0.993
6:152721959:C:A	S138R	0.993
6:152721959:C:G	S138R	0.993
6:152722045:T:C	F167S	0.992
6:152722045:T:G	F167C	0.992
6:152721795:G:A	G84R	0.991
6:152721795:G:C	G84R	0.991
6:152721948:A:C	S135R	0.991
6:152721950:C:A	S135R	0.991
6:152721950:C:G	S135R	0.991
6:152722039:C:A	S165Y	0.991
6:152721953:C:A	N136K	0.990
6:152721953:C:G	N136K	0.990
6:152721975:T:C	F144L	0.990
6:152721977:C:A	F144L	0.990
6:152721977:C:G	F144L	0.990
6:152722026:A:C	S161R	0.990
6:152722028:T:A	S161R	0.990
6:152722028:T:G	S161R	0.990
6:152722029:T:C	F162L	0.990
6:152722031:C:A	F162L	0.990
6:152722031:C:G	F162L	0.990
6:152722239:T:C	F232L	0.989

dbSNP variants (sampled 300 via entrez): RS1000042723 (6:152747349 A>G), RS1000088022 (6:152747207 T>C), RS1000177416 (6:152718175 T>C), RS1000201962 (6:152708296 C>A,T), RS1000254952 (6:152699419 TAAG>T), RS1000333421 (6:152729832 T>C), RS1000419358 (6:152744354 G>A,T), RS1000602442 (6:152696349 T>C), RS1000613848 (6:152719646 A>G), RS1000655017 (6:152695977 A>G), RS1000680808 (6:152725950 C>A,T), RS1000766733 (6:152733662 A>T), RS1000794330 (6:152731083 A>G), RS1000945262 (6:152728463 C>G,T), RS1000984014 (6:152739303 C>A)

Disease associations

OMIM: gene MIM:616805 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

11 associations (top):

Study	Trait	p-value
GCST005951_154	Body mass index	1.000000e-09
GCST008830_19	Neurofibrillary tangles	5.000000e-06
GCST90002385_172	High light scatter reticulocyte count	3.000000e-13
GCST90002386_119	High light scatter reticulocyte percentage of red cells	3.000000e-13
GCST90002388_11	Lymphocyte count	7.000000e-14
GCST90002405_212	Reticulocyte count	3.000000e-11
GCST90002406_231	Reticulocyte fraction of red cells	1.000000e-11
GCST90002407_532	White blood cell count	9.000000e-16
GCST90011898_136	Alanine aminotransferase levels	1.000000e-08
GCST90013405_142	Liver enzyme levels (alanine transaminase)	1.000000e-09
GCST90013407_87	Liver enzyme levels (gamma-glutamyl transferase)	4.000000e-22

EFO canonical traits (5, from GWAS)

EFO ID	Trait name
EFO:0004340	body mass index
EFO:0006797	neurofibrillary tangles measurement
EFO:0007986	reticulocyte count
EFO:0004587	lymphocyte count
EFO:0004532	serum gamma-glutamyl transferase measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

28 total (human), top 28 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, affects expression, increases methylation	7
trichostatin A	increases expression, affects cotreatment	3
sodium arsenite	increases expression	2
Phenylmercuric Acetate	increases expression, affects cotreatment	2
triphenyl phosphate	affects expression	1
2,5,2’,5’-tetrachlorobiphenyl	increases expression	1
2-methyl-4-isothiazolin-3-one	increases expression	1
arsenite	affects binding, increases reaction	1
o,p’-DDT	increases expression	1
butyraldehyde	increases expression	1
mercuric bromide	affects cotreatment, 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	increases expression, affects cotreatment	1
dorsomorphin	affects cotreatment, increases expression	1
bisphenol S	decreases expression	1
prothioconazole	decreases expression	1
(+)-JQ1 compound	decreases expression	1
Panobinostat	affects cotreatment, increases expression	1
Ethanol	decreases expression	1
Benzo(a)pyrene	increases methylation	1
Doxorubicin	decreases expression	1
Polychlorinated Biphenyls	affects expression	1
Thiram	increases expression	1
Tobacco Smoke Pollution	affects expression	1
Triclosan	decreases expression	1
Lithium Chloride	increases expression	1
Antirheumatic Agents	increases expression	1
Cadmium Chloride	increases expression	1

Clinical trials (associated diseases)

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