C1orf56

Summary

C1orf56 (chromosome 1 open reading frame 56, HGNC:26045) is a protein-coding gene on chromosome 1q21.3, encoding Protein MENT (Q9BUN1). Involved in control of cellular proliferation.

This gene is a proto-oncogene whose promoter is methylated by DNA methyltransferase 3B (DNMT3B), which represses the proto-oncogene. However, a catalytically inactive isoform of DNMT3B is overexpressed in lymphomas, leading to hypomethylation of the proto-oncogene’s promoter and derepression of the proto-oncogene.

Source: NCBI Gene 54964 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 9 total
• MANE Select transcript: NM_017860

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26045
Approved symbol	C1orf56
Name	chromosome 1 open reading frame 56
Location	1q21.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ20519, MENT
Ensembl gene	ENSG00000143443
Ensembl biotype	protein_coding
Entrez	54964

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 2 protein_coding_CDS_not_defined, 1 protein_coding

ENST00000368926, ENST00000465135, ENST00000473308

RefSeq mRNA: 1 — MANE Select: NM_017860 NM_017860

CCDS: CCDS980

Canonical transcript exons

ENST00000368926 — 2 exons

Exon	Start	End
ENSE00001448297	151047751	151048852
ENSE00001712848	151050438	151051420

Expression profiles

Bgee: expression breadth ubiquitous, 239 present calls, max score 97.09.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 4.9018 / max 292.7542, expressed in 1468 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
5178	4.7084	1454
5179	0.1935	77

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	97.09	gold quality
right testis	UBERON:0004534	96.68	gold quality
testis	UBERON:0000473	93.27	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	87.64	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	84.40	gold quality
right adrenal gland	UBERON:0001233	84.24	gold quality
adenohypophysis	UBERON:0002196	83.97	gold quality
left adrenal gland cortex	UBERON:0035825	83.90	gold quality
left adrenal gland	UBERON:0001234	83.47	gold quality
right adrenal gland cortex	UBERON:0035827	83.44	gold quality
pituitary gland	UBERON:0000007	82.61	gold quality
adrenal cortex	UBERON:0001235	81.96	gold quality
lower esophagus mucosa	UBERON:0035834	81.82	gold quality
apex of heart	UBERON:0002098	81.44	gold quality
right lobe of thyroid gland	UBERON:0001119	81.42	gold quality
left lobe of thyroid gland	UBERON:0001120	81.14	gold quality
right uterine tube	UBERON:0001302	81.11	gold quality
adrenal gland	UBERON:0002369	80.37	gold quality
secondary oocyte	CL:0000655	80.13	gold quality
oocyte	CL:0000023	80.06	gold quality
thyroid gland	UBERON:0002046	79.87	gold quality
gastrocnemius	UBERON:0001388	79.79	gold quality
right lobe of liver	UBERON:0001114	79.66	gold quality
heart left ventricle	UBERON:0002084	79.46	gold quality
corpus epididymis	UBERON:0004359	79.10	gold quality
body of pancreas	UBERON:0001150	78.99	gold quality
right atrium auricular region	UBERON:0006631	78.92	gold quality
cardiac ventricle	UBERON:0002082	78.86	gold quality
right coronary artery	UBERON:0001625	78.76	gold quality
right ovary	UBERON:0002118	78.76	gold quality

Single-cell (SCXA)

Detected in 7 experiment(s), a significant marker in 4.

Experiment	Marker?	Max mean expression
E-MTAB-8271	yes	823.21
E-HCAD-8	yes	637.68
E-MTAB-3929	yes	192.58
E-ANND-3	yes	4.36
E-MTAB-8498	no	3027.14
E-MTAB-6379	no	2354.52
E-CURD-97	no	1981.89

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

59 targeting C1orf56, 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-6748-5P	100.00	65.81	1057
HSA-MIR-6758-5P	100.00	66.21	1470
HSA-MIR-6856-5P	100.00	65.47	1298
HSA-MIR-6867-5P	100.00	82.21	3464
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-145-5P	99.92	71.13	1836
HSA-MIR-5195-3P	99.92	70.92	1877
HSA-MIR-10527-5P	99.91	72.28	3754
HSA-MIR-1305	99.91	71.43	3443
HSA-MIR-3671	99.90	73.04	3897
HSA-MIR-605-3P	99.88	69.22	1833
HSA-MIR-4503	99.85	71.45	1869
HSA-MIR-498-5P	99.76	69.64	1807
HSA-MIR-6745	99.74	65.33	1321
HSA-MIR-3659	99.70	67.97	694
HSA-MIR-5093	99.67	69.26	2291
HSA-MIR-488-3P	99.61	68.79	1731
HSA-MIR-6716-5P	99.56	68.62	1244
HSA-MIR-5004-3P	99.54	68.27	1371
HSA-MIR-6832-3P	99.52	70.44	1726
HSA-MIR-3609	99.52	69.89	2587
HSA-MIR-548AH-5P	99.52	69.73	2626
HSA-MIR-6083	99.47	68.73	2393
HSA-MIR-363-5P	99.46	64.51	1015
HSA-MIR-3915	99.45	68.49	1905
HSA-MIR-2392	99.43	67.50	708
HSA-MIR-942-5P	99.41	68.40	1977

Literature-anchored findings (GeneRIF, showing 1)

• DNMT3B7 overexpression might interfere with the normal DNA methylation mechanism required for silencing the MENT proto-oncogene, and may accelerate human lymphomagenesis. (PMID:24094886)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Gm128	ENSMUSG00000068860
rattus_norvegicus	C2h1orf56	ENSRNOG00000021656

Protein

Protein identifiers

Protein MENT — Q9BUN1 (reviewed: Q9BUN1)

Alternative names: Methylated in normal thymocytes protein

All UniProt accessions (1): Q9BUN1

UniProt curated annotations — full annotation on UniProt →

Function. Involved in control of cellular proliferation. Onconcogenic modifier contributing to the tumor suppressor function of DNMT3B.

Subcellular location. Secreted.

Tissue specificity. Plasma. Overexpressed in lymphomas.

Post-translational modifications. Phosphorylation sites are present in the extracellular medium.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9BUN1-1	1	yes
Q9BUN1-2	2

RefSeq proteins (1): NP_060330* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR029292	MENT	Family

Pfam: PF15322

UniProt features (6 total): splice variant 2, signal peptide 1, 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-Q9BUN1-F1	52.75	0.09

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 69 (showing top): NUYTTEN_EZH2_TARGETS_DN, chr1q21, MIKKELSEN_ES_ICP_WITH_H3K4ME3, LIM_MAMMARY_STEM_CELL_DN, MTOR_UP.N4.V1_DN, H1_6_TARGET_GENES, SUPT16H_TARGET_GENES, ZBTB12_TARGET_GENES, MIR607, MIR3671, MIR10527_5P, MIR942_5P, MIR4279, MIR5691_MIR6805_3P, MIR6738_3P

GO Biological Process (1): regulation of cell population proliferation (GO:0042127)

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

GO Cellular Component (1): extracellular region (GO:0005576)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cell population proliferation	1
regulation of cellular process	1
binding	1
cellular anatomical structure	1

Protein interactions and networks

STRING

186 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
C1orf56	CDC42SE1	Q9NRR8	433
C1orf56	NOXRED1	Q6NXP6	406
C1orf56	LENG1	Q96BZ8	372
C1orf56	C6orf89	Q6UWU4	371
C1orf56	PPP1R27	Q86WC6	360
C1orf56	TMEM89	A2RUT3	339
C1orf56	C16orf54	Q6UWD8	321
C1orf56	SPACA1	Q9HBV2	311
C1orf56	MLLT11	Q13015	306
C1orf56	IQCF5	A8MTL0	288
C1orf56	RSPH6A	Q9H0K4	285
C1orf56	ZPBP	Q9BS86	272
C1orf56	KCNMB3	Q9NPA1	269
C1orf56	DPEP3	Q9H4B8	259
C1orf56	ARSA	P15289	255

IntAct

17 interactions, top by confidence:

A	B	Type	Score
TCF4	MENT	psi-mi:“MI:0915”(physical association)	0.560
REL	MENT	psi-mi:“MI:0915”(physical association)	0.560
CRX	MENT	psi-mi:“MI:0915”(physical association)	0.560
COX20	MENT	psi-mi:“MI:0915”(physical association)	0.560
INCA1	MENT	psi-mi:“MI:0915”(physical association)	0.560
MENT	FAM20C	psi-mi:“MI:0217”(phosphorylation reaction)	0.440
MENT	TCF4	psi-mi:“MI:0915”(physical association)	0.000
MENT	REL	psi-mi:“MI:0915”(physical association)	0.000
MENT	CRX	psi-mi:“MI:0915”(physical association)	0.000
MENT	COX20	psi-mi:“MI:0915”(physical association)	0.000
MENT	INCA1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (5): C1orf56 (Two-hybrid), REL (Two-hybrid), INCA1 (Two-hybrid), TCF4 (Two-hybrid), COX20 (Two-hybrid)

ESM2 similar proteins: A1KXC4, B2RQL2, B2RTN2, O35188, O55145, O60667, O95196, P06484, P07141, P16382, P24394, P25918, P78423, Q29RT9, Q3SYS8, Q58CT8, Q5BK39, Q5FVQ5, Q5M871, Q5U2P6, Q63257, Q64322, Q68CR7, Q68DV7, Q6AXU5, Q6P1B3, Q6PNM1, Q6RFH4, Q71M36, Q863Z5, Q8BHB3, Q8BHE4, Q8BHW6, Q8BSU2, Q8C708, Q8IXW0, Q8JZQ0, Q8K0B3, Q8NET5, Q8R183

Diamond homologs: Q569E4, Q5XI62, Q9BUN1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	3
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

380 predictions. Top by Δscore:

Variant	Effect	Δscore
1:151048853:G:GG	donor_gain	0.9800
1:151048849:ACCA:A	donor_gain	0.9700
1:151050652:C:G	donor_gain	0.9700
1:151048851:CA:C	donor_gain	0.9500
1:151048850:CCA:C	donor_gain	0.9300
1:151050129:G:GT	donor_gain	0.9300
1:151048851:CAGT:C	donor_loss	0.9000
1:151048852:AGTAA:A	donor_loss	0.9000
1:151048854:TAAG:T	donor_loss	0.9000
1:151048855:A:AC	donor_loss	0.9000
1:151048856:AGTGT:A	donor_loss	0.9000
1:151050436:A:AG	acceptor_gain	0.9000
1:151050437:G:GG	acceptor_gain	0.9000
1:151050437:GATA:G	acceptor_gain	0.8900
1:151048154:G:GT	donor_gain	0.8700
1:151050187:T:TA	donor_gain	0.8600
1:151050188:A:AA	donor_gain	0.8600
1:151048848:AACCA:A	donor_gain	0.8400
1:151050437:GAT:G	acceptor_gain	0.8300
1:151050433:C:CA	acceptor_gain	0.8200
1:151048136:T:TA	donor_gain	0.7900
1:151050105:G:GT	donor_gain	0.7900
1:151048696:G:GT	donor_gain	0.7600
1:151048867:A:AG	donor_gain	0.7600
1:151050433:C:G	acceptor_gain	0.7600
1:151050130:A:T	donor_gain	0.7300
1:151050434:GCA:G	acceptor_loss	0.7300
1:151050435:CA:C	acceptor_loss	0.7300
1:151050436:A:G	acceptor_loss	0.7300
1:151050437:G:GT	acceptor_loss	0.7300

AlphaMissense

2190 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:151048474:G:C	W209C	0.999
1:151048474:G:T	W209C	0.999
1:151048465:G:C	W206C	0.998
1:151048465:G:T	W206C	0.998
1:151048472:T:A	W209R	0.997
1:151048472:T:C	W209R	0.997
1:151048478:T:A	C211S	0.996
1:151048479:G:C	C211S	0.996
1:151048480:C:G	C211W	0.996
1:151048631:T:A	C262S	0.996
1:151048632:G:C	C262S	0.996
1:151048484:T:A	C213S	0.995
1:151048485:G:C	C213S	0.995
1:151048589:T:A	C248S	0.995
1:151048590:G:C	C248S	0.995
1:151048631:T:C	C262R	0.995
1:151048463:T:A	W206R	0.994
1:151048463:T:C	W206R	0.994
1:151048478:T:C	C211R	0.994
1:151048479:G:A	C211Y	0.994
1:151048485:G:A	C213Y	0.994
1:151048591:C:G	C248W	0.994
1:151048783:G:C	W312C	0.994
1:151048783:G:T	W312C	0.994
1:151048486:C:G	C213W	0.993
1:151048589:T:C	C248R	0.993
1:151048590:G:A	C248Y	0.993
1:151048610:T:A	C255S	0.993
1:151048611:G:C	C255S	0.993
1:151048479:G:T	C211F	0.992

dbSNP variants (sampled 300 via entrez): RS1000588042 (1:151047699 G>A,C), RS1001756962 (1:151051659 G>C), RS1002214386 (1:151046467 G>A), RS1003653465 (1:151046287 T>C), RS1003842647 (1:151050071 C>T), RS1004004131 (1:151046992 G>A), RS1004507711 (1:151046563 T>C,G), RS1005161065 (1:151046811 C>T), RS1005435066 (1:151047143 G>A), RS1006566232 (1:151047802 G>C), RS1007267537 (1:151050649 T>C), RS1007519242 (1:151049318 T>C), RS1007879663 (1:151049573 C>A,T), RS1008300887 (1:151047685 C>G,T), RS1008474294 (1:151051457 G>C)

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

1 associations (top):

Study	Trait	p-value
GCST006585_2851	Blood protein levels	9.000000e-09

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

20 total (human), top 20 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, affects expression	3
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
sodium arsenite	decreases expression	1
butyraldehyde	decreases 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	affects cotreatment, decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Sunitinib	decreases expression	1
Arsenic	affects methylation	1
Benzo(a)pyrene	affects methylation	1
Ivermectin	increases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Silver	increases expression	1
Smoke	decreases expression	1
Tretinoin	increases expression	1
Urethane	increases expression	1
Okadaic Acid	decreases expression	1
Lactic Acid	decreases expression	1
Particulate Matter	decreases expression	1

Clinical trials (associated diseases)

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