C1orf52

Summary

C1orf52 (chromosome 1 open reading frame 52, HGNC:24871) is a protein-coding gene on chromosome 1p22.3, encoding UPF0690 protein C1orf52 (Q8N6N3).

Enables RNA binding activity. Located in nucleoplasm.

Source: NCBI Gene 148423 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 1 total
• MANE Select transcript: NM_198077

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24871
Approved symbol	C1orf52
Name	chromosome 1 open reading frame 52
Location	1p22.3
Locus type	gene with protein product
Status	Approved
Aliases	gm117, FLJ44982
Ensembl gene	ENSG00000162642
Ensembl biotype	protein_coding
Entrez	148423

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 3 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000294661, ENST00000344356, ENST00000471115, ENST00000493514, ENST00000881334

RefSeq mRNA: 1 — MANE Select: NM_198077 NM_198077

CCDS: CCDS703

Canonical transcript exons

ENST00000471115 — 3 exons

Exon	Start	End
ENSE00001384996	85259358	85259662
ENSE00001854391	85249953	85252702
ENSE00003604451	85258524	85258722

Expression profiles

Bgee: expression breadth ubiquitous, 259 present calls, max score 95.32.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 41.9038 / max 271.3708, expressed in 1821 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
13022	41.9038	1821

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
upper arm skin	UBERON:0004263	95.32	gold quality
epithelial cell of pancreas	CL:0000083	94.22	gold quality
oviduct epithelium	UBERON:0004804	93.72	gold quality
Brodmann (1909) area 46	UBERON:0006483	93.64	gold quality
amniotic fluid	UBERON:0000173	93.62	gold quality
Brodmann (1909) area 23	UBERON:0013554	93.37	gold quality
thymus	UBERON:0002370	93.33	gold quality
endothelial cell	CL:0000115	93.00	silver quality
left ventricle myocardium	UBERON:0006566	92.96	gold quality
tibia	UBERON:0000979	92.74	gold quality
germinal epithelium of ovary	UBERON:0001304	92.74	gold quality
prefrontal cortex	UBERON:0000451	92.56	gold quality
tibialis anterior	UBERON:0001385	92.41	gold quality
cartilage tissue	UBERON:0002418	92.22	gold quality
middle temporal gyrus	UBERON:0002771	92.04	gold quality
superior frontal gyrus	UBERON:0002661	91.98	gold quality
gingival epithelium	UBERON:0001949	91.78	gold quality
postcentral gyrus	UBERON:0002581	91.73	gold quality
layer of synovial tissue	UBERON:0007616	91.50	gold quality
cardiac muscle of right atrium	UBERON:0003379	91.29	silver quality
entorhinal cortex	UBERON:0002728	91.28	gold quality
palpebral conjunctiva	UBERON:0001812	91.22	gold quality
deltoid	UBERON:0001476	91.14	silver quality
epithelium of nasopharynx	UBERON:0001951	91.11	gold quality
parietal lobe	UBERON:0001872	91.10	gold quality
placenta	UBERON:0001987	91.09	gold quality
monocyte	CL:0000576	91.02	gold quality
upper leg skin	UBERON:0004262	91.02	gold quality
ileal mucosa	UBERON:0000331	90.96	gold quality
myocardium	UBERON:0002349	90.91	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.92

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

122 targeting C1orf52, 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-3163	100.00	77.23	8605
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-3924	100.00	72.09	2394
HSA-MIR-5193	100.00	67.26	1744
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-3662	99.99	73.82	5684
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-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-9985	99.98	72.11	2939
HSA-LET-7F-2-3P	99.98	70.98	2588
HSA-MIR-1185-1-3P	99.98	71.04	2593
HSA-MIR-1185-2-3P	99.98	71.04	2593
HSA-MIR-499A-5P	99.98	70.79	1323
HSA-MIR-4789-5P	99.98	70.76	2721
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-2110	99.96	66.68	1930
HSA-MIR-128-3P	99.95	71.17	2484
HSA-MIR-216A-3P	99.95	71.19	2505
HSA-LET-7C-3P	99.95	73.42	2862

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	C23H1orf52	ENSDARG00000103134
mus_musculus	2410004B18Rik	ENSMUSG00000036873
rattus_norvegicus	C2h1orf52	ENSRNOG00000014857

Protein

Protein identifiers

UPF0690 protein C1orf52 — Q8N6N3 (reviewed: Q8N6N3)

Alternative names: BCL10-associated gene protein

All UniProt accessions (1): Q8N6N3

UniProt curated annotations — full annotation on UniProt →

Tissue specificity. Expressed in all tissues tested including heart, placenta, liver, skeletal muscle, kidney and pancreas. Weak expression in brain and lung.

Similarity. Belongs to the UPF0690 family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q8N6N3-1	1	yes
Q8N6N3-2	2, GM117 form A
Q8N6N3-3	3, GM117 form B

RefSeq proteins (1): NP_932343* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR029089	DUF4660	Family

Pfam: PF15559

UniProt features (14 total): splice variant 4, compositionally biased region 4, modified residue 3, region of interest 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N6N3-F1	62.48	0.00

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 (3): 67, 132, 158

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 102 (showing top): GCM_NUMA1, LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN, GCM_NF2, chr1p22, GCM_CSNK1A1, MARTENS_TRETINOIN_RESPONSE_DN, GCM_MLL, CSR_LATE_UP.V1_DN, GCM_DENR, GSE13522_WT_VS_IFNAR_KO_SKING_T_CRUZI_Y_STRAIN_INF_DN, ELF2_TARGET_GENES, HOXB4_TARGET_GENES, KAT5_TARGET_GENES, TOP2B_TARGET_GENES, ZNF768_TARGET_GENES

GO Biological Process (0):

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

GO Cellular Component (1): nucleoplasm (GO:0005654)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
nucleic acid binding	1
nuclear lumen	1
cellular anatomical structure	1

Protein interactions and networks

STRING

196 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
C1orf52	SYDE2	Q5VT97	477
C1orf52	ZNHIT6	Q9NWK9	447
C1orf52	RBM33	Q96EV2	446
C1orf52	UTP25	Q68CQ4	419
C1orf52	CENATAC	Q86UT8	397
C1orf52	TMEM208	Q9BTX3	385
C1orf52	DDAH1	O94760	370
C1orf52	ESYT2	A0FGR8	356
C1orf52	ZNF585A	Q6P3V2	350
C1orf52	NDFIP2	Q9NV92	350
C1orf52	SCAMP1	O15126	336
C1orf52	SSR1	P43307	318
C1orf52	MRGBP	Q9NV56	318
C1orf52	CCDC122	Q5T0U0	293
C1orf52	ZNF585B	Q52M93	290

IntAct

45 interactions, top by confidence:

A	B	Type	Score
MED17	MED19	psi-mi:“MI:0914”(association)	0.840
LMO1	ZBTB43	psi-mi:“MI:0914”(association)	0.830
PRPF19	AQR	psi-mi:“MI:0914”(association)	0.790
MAD2L1BP	LBR	psi-mi:“MI:0914”(association)	0.730
MAD2L1	INSR	psi-mi:“MI:0914”(association)	0.700
GPX7	GAK	psi-mi:“MI:0914”(association)	0.640
Mad2l1	BUB1B	psi-mi:“MI:0915”(physical association)	0.560
DEF6	ARHGAP42	psi-mi:“MI:0914”(association)	0.530
BAG2	HGS	psi-mi:“MI:0914”(association)	0.530
LHX4	THAP12	psi-mi:“MI:0914”(association)	0.530
MAD2L1BP	KIF20A	psi-mi:“MI:0914”(association)	0.530
MAD2L1	PPIP5K2	psi-mi:“MI:0914”(association)	0.530
C1orf52	Dlg4	psi-mi:“MI:0407”(direct interaction)	0.440
C1orf52	COX4I1	psi-mi:“MI:0915”(physical association)	0.400
Mad2l1	MAD1L1	psi-mi:“MI:0914”(association)	0.350
Snw1	AKR7A2	psi-mi:“MI:0914”(association)	0.350
CEP170P1	PCYT1A	psi-mi:“MI:0914”(association)	0.350
Crnkl1	PLRG1	psi-mi:“MI:0914”(association)	0.350
Isy1	PFDN6	psi-mi:“MI:0914”(association)	0.350
KIF20B	ACSL3	psi-mi:“MI:0914”(association)	0.350
Kifbp	TPM1	psi-mi:“MI:0914”(association)	0.350
RNASEH2B	SAP18	psi-mi:“MI:0914”(association)	0.350
Vps4b	CNOT1	psi-mi:“MI:0914”(association)	0.350
Chmp6	NSF	psi-mi:“MI:0914”(association)	0.350
RAB5A	ENTPD6	psi-mi:“MI:0914”(association)	0.350
CLCN2	PEX10	psi-mi:“MI:0914”(association)	0.350
FAN1		psi-mi:“MI:0914”(association)	0.350
CHMP4B		psi-mi:“MI:0914”(association)	0.350
hspa1a_hspa1b_human-1	SHTN1	psi-mi:“MI:0914”(association)	0.350
MAD2L1	MED19	psi-mi:“MI:0914”(association)	0.350

BioGRID (85): C1orf52 (Affinity Capture-MS), C1orf52 (Affinity Capture-MS), C1orf52 (Affinity Capture-MS), C1orf52 (Proximity Label-MS), C1orf52 (Affinity Capture-MS), C1orf52 (Affinity Capture-MS), C1orf52 (Affinity Capture-MS), C1orf52 (Affinity Capture-MS), C1orf52 (Affinity Capture-MS), C1orf52 (Affinity Capture-MS), C1orf52 (Affinity Capture-MS), C1orf52 (Affinity Capture-MS), C1orf52 (Affinity Capture-MS), C1orf52 (Affinity Capture-MS), C1orf52 (Affinity Capture-MS)

ESM2 similar proteins: A0JNL1, A1L2F3, A6H7J2, A9C3N6, B5G1P1, B5X7E4, B5XBI1, E7F5E1, O14279, P58468, P86346, Q07FY3, Q0P4A6, Q28E54, Q28IC1, Q2TBN9, Q2YDJ0, Q3UY34, Q58CQ0, Q5BK57, Q5EAY2, Q5FWN9, Q5I034, Q5ZMG5, Q62627, Q751T1, Q7TT28, Q7ZWE7, Q80VC9, Q86WX3, Q8C3W1, Q8C5R2, Q8C6B9, Q8K0S9, Q8N1G1, Q8N6N3, Q8NEG2, Q8WUQ7, Q96C57, Q96FT9

Diamond homologs: Q28E54, Q32LF5, Q32NA2, Q5FWN9, Q7SZP2, Q8N6N3, Q9CWU4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

1 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

634 predictions. Top by Δscore:

Variant	Effect	Δscore
1:85259359:T:TA	donor_gain	1.0000
1:85252700:CAT:C	acceptor_gain	0.9900
1:85252703:C:CC	acceptor_gain	0.9900
1:85252704:T:C	acceptor_gain	0.9900
1:85252705:T:C	acceptor_gain	0.9900
1:85252709:A:AC	acceptor_gain	0.9900
1:85257234:T:C	acceptor_gain	0.9900
1:85258518:CCTTA:C	donor_loss	0.9900
1:85258519:CTTAC:C	donor_loss	0.9900
1:85258520:TTACC:T	donor_loss	0.9900
1:85258521:TACCT:T	donor_loss	0.9900
1:85258522:A:T	donor_loss	0.9900
1:85258523:C:A	donor_loss	0.9900
1:85258723:C:CC	acceptor_gain	0.9900
1:85259352:CCTCA:C	donor_loss	0.9900
1:85259353:CTCAC:C	donor_loss	0.9900
1:85259354:TCA:T	donor_loss	0.9900
1:85259355:CA:C	donor_loss	0.9900
1:85259356:A:AG	donor_loss	0.9900
1:85259356:ACCT:A	donor_gain	0.9900
1:85259357:CCTC:C	donor_gain	0.9900
1:85252701:ATCT:A	acceptor_loss	0.9800
1:85252702:TCTT:T	acceptor_loss	0.9800
1:85252704:T:A	acceptor_loss	0.9800
1:85252705:T:TC	acceptor_gain	0.9800
1:85252709:A:C	acceptor_gain	0.9800
1:85253650:TTAC:T	donor_gain	0.9800
1:85257233:C:CC	acceptor_gain	0.9800
1:85258517:T:A	donor_gain	0.9800
1:85257229:CAGA:C	acceptor_gain	0.9700

AlphaMissense

1203 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:85258615:C:A	W128C	0.999
1:85258615:C:G	W128C	0.999
1:85258617:A:G	W128R	0.999
1:85258617:A:T	W128R	0.999
1:85259388:C:A	W82C	0.999
1:85259388:C:G	W82C	0.999
1:85259390:A:G	W82R	0.998
1:85259390:A:T	W82R	0.998
1:85259421:A:C	F71L	0.998
1:85259421:A:T	F71L	0.998
1:85259423:A:G	F71L	0.998
1:85258618:T:A	K127N	0.996
1:85258618:T:G	K127N	0.996
1:85258616:C:G	W128S	0.995
1:85259389:C:G	W82S	0.995
1:85259422:A:G	F71S	0.995
1:85258613:G:A	S129F	0.994
1:85258614:A:G	S129P	0.994
1:85258622:A:T	I126K	0.994
1:85259598:A:C	F12L	0.994
1:85259598:A:T	F12L	0.994
1:85259600:A:G	F12L	0.994
1:85258708:G:C	F97L	0.993
1:85258708:G:T	F97L	0.993
1:85258710:A:G	F97L	0.993
1:85258599:C:G	D134H	0.992
1:85259428:G:T	P69Q	0.992
1:85258622:A:C	I126R	0.991
1:85258625:G:T	A125E	0.991
1:85259599:A:G	F12S	0.991

dbSNP variants (sampled 300 via entrez): RS1000228999 (1:85253500 T>C), RS1000262593 (1:85259715 G>A,T), RS1001007404 (1:85256327 T>C), RS1001357051 (1:85253394 C>T), RS1001527180 (1:85259142 C>G,T), RS1001561608 (1:85258877 T>C), RS1001747696 (1:85257872 G>A), RS1001830206 (1:85252947 T>C), RS1002339485 (1:85254438 A>C), RS1002387573 (1:85259670 G>A), RS1003047417 (1:85259070 G>A,C,T), RS1003058483 (1:85251537 G>A), RS1003234239 (1:85257592 T>C,G), RS1003435830 (1:85251906 G>A), RS1003621030 (1:85254217 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

2 associations (top):

Study	Trait	p-value
GCST009391_1900	Metabolite levels	3.000000e-06
GCST009597_75	Multiple sclerosis	2.000000e-31

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0010454	adenosine monophosphate measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	affects expression, increases expression	2
Tobacco Smoke Pollution	increases expression	2
Valproic Acid	affects expression, decreases methylation, increases expression	2
Zinc	decreases expression, affects cotreatment, increases expression	2
FR900359	increases phosphorylation	1
dicrotophos	decreases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	increases expression	1
2-methyl-4-isothiazolin-3-one	increases expression	1
cobaltous chloride	increases expression	1
butyraldehyde	increases expression	1
potassium chromate(VI)	affects cotreatment, increases expression	1
coumarin	decreases phosphorylation	1
epigallocatechin gallate	affects cotreatment, increases expression	1
2-palmitoylglycerol	increases expression	1
abrine	increases expression	1
(4-amino-1,4-dihydro-3-(2-pyridyl)-5-thioxo-1,2,4-triazole)copper(II)	increases expression	1
PCI 5002	affects cotreatment, increases expression	1
Resveratrol	affects cotreatment, increases expression	1
Temozolomide	increases expression	1
Acetaminophen	increases expression	1
Air Pollutants	increases abundance, decreases expression	1
Benzo(a)pyrene	affects methylation	1
Enzyme Inhibitors	decreases activity, increases O-linked glycosylation	1
Plant Extracts	affects cotreatment, increases expression	1
Plant Oils	increases expression	1
Ribonucleotides	affects binding	1
Silver	increases expression	1
Smoke	decreases expression	1
Sulindac	increases expression	1

Clinical trials (associated diseases)

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