MCTS2

Summary

MCTS2 (MCTS family member 2, HGNC:49760) is a protein-coding gene on chromosome 20q11.21, encoding Malignant T-cell-amplified sequence 2 (A0A3B3IRV3).

This locus represents a retrogene copy of MCTS1 (GeneID:28985) and contains an ORF similar to that parent gene. This locus is situated in a differentially methylated region (DMR) and transcripts in this region are imprinted.

Source: NCBI Gene 100101490 — RefSeq curated summary.

At a glance

• MANE Select transcript: NM_001397496

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:49760
Approved symbol	MCTS2
Name	MCTS family member 2
Location	20q11.21
Locus type	gene with protein product
Status	Approved
Aliases	psiMCT-1
Ensembl gene	ENSG00000101898
Ensembl biotype	protein_coding
OMIM	620406
Entrez	100101490

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 4 nonsense_mediated_decay, 2 protein_coding

ENST00000394552, ENST00000464508, ENST00000464661, ENST00000479096, ENST00000487964, ENST00000718306

RefSeq mRNA: 1 — MANE Select: NM_001397496 NM_001397496

CCDS: CCDS93025

Canonical transcript exons

ENST00000394552 — 1 exons

Exon	Start	End
ENSE00001454928	31547379	31548081

Expression profiles

Bgee: expression breadth ubiquitous, 129 present calls, max score 85.20.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 13.1235 / max 415.4982, expressed in 1674 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
183964	13.1235	1674

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	85.20	gold quality
cortical plate	UBERON:0005343	77.06	gold quality
tonsil	UBERON:0002372	74.04	gold quality
islet of Langerhans	UBERON:0000006	73.75	gold quality
endometrium	UBERON:0001295	70.29	gold quality
bone marrow cell	CL:0002092	69.98	gold quality
ganglionic eminence	UBERON:0004023	69.42	gold quality
placenta	UBERON:0001987	69.00	gold quality
smooth muscle tissue	UBERON:0001135	67.75	gold quality
lower esophagus mucosa	UBERON:0035834	66.41	gold quality
vermiform appendix	UBERON:0001154	64.35	gold quality
lymph node	UBERON:0000029	64.15	gold quality
adrenal tissue	UBERON:0018303	64.02	gold quality
corpus callosum	UBERON:0002336	63.98	gold quality
bone marrow	UBERON:0002371	63.42	gold quality
rectum	UBERON:0001052	62.52	gold quality
duodenum	UBERON:0002114	62.29	gold quality
right adrenal gland cortex	UBERON:0035827	61.38	gold quality
esophagus mucosa	UBERON:0002469	61.10	gold quality
right ovary	UBERON:0002118	59.46	gold quality
metanephros cortex	UBERON:0010533	59.34	gold quality
vagina	UBERON:0000996	59.03	gold quality
urinary bladder	UBERON:0001255	58.95	gold quality
right adrenal gland	UBERON:0001233	58.45	gold quality
ovary	UBERON:0000992	58.02	gold quality
gall bladder	UBERON:0002110	57.85	gold quality
pancreas	UBERON:0001264	57.59	gold quality
esophagus	UBERON:0001043	56.88	gold quality
fallopian tube	UBERON:0003889	56.74	gold quality
adenohypophysis	UBERON:0002196	56.71	gold quality

Single-cell (SCXA)

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

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

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 1)

• A pseudogene for MCT-1 (PsiMCT-1) that is located on chromosome 20q11.2 was identified. (PMID:16815567)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	mcts1	ENSDARG00000025972
drosophila_melanogaster	MCTS1	FBGN0029833
caenorhabditis_elegans		WBGENE00015703

Paralogs (1): MCTS1 (ENSG00000232119)

Protein

Protein identifiers

Malignant T-cell-amplified sequence 2 — A0A3B3IRV3 (reviewed: A0A3B3IRV3)

All UniProt accessions (1): A0A3B3IRV3

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Cytoplasm.

Miscellaneous. Imprinted gene expressed from the paternal allele in fetal spinal cord.

Similarity. Belongs to the MCTS1 family.

RefSeq proteins (1): NP_001384425* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002478	PUA	Domain
IPR004521	Uncharacterised_CHP00451	Domain
IPR015947	PUA-like_sf	Homologous_superfamily
IPR016437	MCT-1/Tma20	Family
IPR041366	Pre-PUA	Domain

Pfam: PF01472, PF17832

UniProt features (2 total): chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A0A3B3IRV3-F1	96.59	0.98

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 19 (showing top): GOBP_CYTOPLASMIC_TRANSLATION, IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR, GOBP_TRANSLATIONAL_INITIATION, GOBP_TRANSLATION, GOBP_FORMATION_OF_TRANSLATION_PREINITIATION_COMPLEX, GOBP_CYTOPLASMIC_TRANSLATIONAL_INITIATION, GOBP_PROTEIN_RNA_COMPLEX_ORGANIZATION, chr20q11, GOBP_RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS, LEE_BMP2_TARGETS_DN, BRIDEAU_IMPRINTED_GENES, FOXR2_TARGET_GENES, GUCY1B1_TARGET_GENES, LHX2_TARGET_GENES, ZNF134_TARGET_GENES

GO Biological Process (2): formation of translation preinitiation complex (GO:0001731), translation reinitiation (GO:0002188)

GO Molecular Function (1): RNA binding (GO:0003723)

GO Cellular Component (1): cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cytoplasmic translational initiation	2
protein-RNA complex assembly	1
nucleic acid binding	1
intracellular anatomical structure	1
cellular anatomical structure	1

Protein interactions and networks

STRING

358 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
MCTS2	NAP1L5	Q96NT1	720
MCTS2	HM13	Q8TCT9	613
MCTS2	ZDBF2	Q9HCK1	600
MCTS2	FAM50B	Q9Y247	591
MCTS2	PEG10	Q86TG7	581
MCTS2	NNAT	Q16517	571
MCTS2	MEST	Q5EB52	542
MCTS2	WDR20	Q8TBZ3	480
MCTS2	PEG3	P78418	479
MCTS2	L3MBTL1	Q9Y468	474
MCTS2	SVOPL	Q8N434	474
MCTS2	SNRPN	P14648	472
MCTS2	ZNF331	Q9NQX6	447
MCTS2	GNAS	Q5JWF2	447
MCTS2	HERC3	Q15034	447

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A3B3IRV3, A0SXL6, A5DK38, A5PKR8, B6K286, O13914, O14179, P05197, P09445, P13188, P13639, P14325, P29691, P55823, P58252, P87313, P89886, Q07803, Q07953, Q09191, Q23716, Q25566, Q2KIE4, Q3SYU2, Q4G009, Q54Y20, Q554D9, Q5PPY1, Q5R8Z3, Q5ZI42, Q6BIJ0, Q6BPD3, Q6CA26, Q6CJ62, Q6DER1, Q6NRJ7, Q6P3J5, Q75AA8, Q75CZ5, Q7ZV34

Diamond homologs: A0A3B3IRV3, P87313, P89886, Q2KIE4, Q4G009, Q58827, Q5PPY1, Q5ZI42, Q6DER1, Q6NRJ7, Q75AA8, Q7ZV34, Q86KL4, Q9CQ21, Q9DB27, Q9ULC4, Q9W445, P0CL18, P41214, Q5RA63, B6YUR8, O57712, Q57878, Q5JHC0, Q8TH90, Q58CR3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

0 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	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1556 predictions. Top by Δscore:

Variant	Effect	Δscore
20:31549110:GGAAG:G	donor_gain	1.0000
20:31549111:GAAG:G	donor_gain	1.0000
20:31549111:GAAGG:G	donor_gain	1.0000
20:31549112:A:T	donor_gain	1.0000
20:31549112:AAGGT:A	donor_loss	1.0000
20:31549113:AG:A	donor_gain	1.0000
20:31549114:GG:G	donor_gain	1.0000
20:31549115:G:A	donor_loss	1.0000
20:31549115:G:GG	donor_gain	1.0000
20:31549205:A:AG	acceptor_gain	1.0000
20:31549206:G:GG	acceptor_gain	1.0000
20:31549206:GCACT:G	acceptor_gain	1.0000
20:31549331:GG:G	donor_gain	1.0000
20:31549332:GG:G	donor_gain	1.0000
20:31549332:GGT:G	donor_loss	1.0000
20:31549334:T:A	donor_loss	1.0000
20:31550059:TCTA:T	acceptor_loss	1.0000
20:31550061:TA:T	acceptor_loss	1.0000
20:31550062:A:AG	acceptor_gain	1.0000
20:31550062:A:G	acceptor_loss	1.0000
20:31550062:AG:A	acceptor_gain	1.0000
20:31550063:G:GT	acceptor_gain	1.0000
20:31550063:GG:G	acceptor_gain	1.0000
20:31550063:GGT:G	acceptor_gain	1.0000
20:31550063:GGTA:G	acceptor_gain	1.0000
20:31550063:GGTAT:G	acceptor_gain	1.0000
20:31550117:AAAAT:A	donor_gain	1.0000
20:31550118:AAAT:A	donor_gain	1.0000
20:31550119:AAT:A	donor_gain	1.0000
20:31550120:AT:A	donor_gain	1.0000

AlphaMissense

1202 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
20:31547813:T:C	F104L	0.998
20:31547815:T:A	F104L	0.998
20:31547815:T:G	F104L	0.998
20:31547850:T:C	L116S	0.995
20:31547904:T:A	V134D	0.994
20:31547940:G:A	G146E	0.994
20:31548026:T:A	W175R	0.994
20:31548026:T:C	W175R	0.994
20:31547939:G:T	G146W	0.993
20:31547556:A:T	K18I	0.992
20:31548017:G:C	D172H	0.992
20:31547826:G:T	G108V	0.991
20:31547847:G:A	G115D	0.991
20:31547937:T:A	V145D	0.991
20:31548018:A:T	D172V	0.991
20:31547826:G:A	G108D	0.990
20:31547839:G:A	M112I	0.990
20:31547839:G:C	M112I	0.990
20:31547839:G:T	M112I	0.990
20:31547842:T:G	C113W	0.990
20:31547991:G:A	G163D	0.990
20:31547817:T:A	V105E	0.989
20:31547898:T:A	V132E	0.989
20:31548018:A:C	D172A	0.989
20:31547796:A:T	D98V	0.988
20:31547939:G:A	G146R	0.988
20:31547939:G:C	G146R	0.988
20:31548019:T:A	D172E	0.988
20:31548019:T:G	D172E	0.988
20:31547759:C:G	H86D	0.987

dbSNP variants (sampled 300 via entrez): RS1000898968 (20:31547475 C>A,G), RS1000917712 (20:31545672 A>G), RS1002926629 (20:31548465 G>A), RS1003430132 (20:31545783 G>A), RS1003920231 (20:31547380 G>A), RS1003993126 (20:31546088 C>A,T), RS1004995884 (20:31548154 T>C), RS1007785847 (20:31546341 ACT>A), RS1007996634 (20:31546526 G>A), RS1008067086 (20:31547411 C>T), RS1008116334 (20:31547694 T>C), RS1008360183 (20:31546814 A>G), RS1010179779 (20:31547170 C>T), RS1010249444 (20:31545715 C>T), RS1010478122 (20:31547388 G>A)

Disease associations

OMIM: gene MIM:620406 | 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)

CTD chemical–gene interactions

4 total (human), top 4 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
jinfukang	affects cotreatment, decreases expression	1
Sunitinib	increases expression	1
Cisplatin	affects cotreatment, decreases expression	1
Estradiol	increases expression	1

Clinical trials (associated diseases)

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