C3orf18

Summary

C3orf18 (chromosome 3 open reading frame 18, HGNC:24837) is a protein-coding gene on chromosome 3p21.31, encoding Uncharacterized protein C3orf18 (Q9UK00).

Predicted to be located in membrane.

Source: NCBI Gene 51161 — RefSeq curated summary.

At a glance

• GWAS associations: 7
• Clinical variants (ClinVar): 30 total
• MANE Select transcript: NM_016210

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24837
Approved symbol	C3orf18
Name	chromosome 3 open reading frame 18
Location	3p21.31
Locus type	gene with protein product
Status	Approved
Aliases	G20
Ensembl gene	ENSG00000088543
Ensembl biotype	protein_coding
Entrez	51161

Gene structure

Transcript identifiers

Ensembl transcripts: 28 — 22 protein_coding, 5 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000357203, ENST00000422619, ENST00000426034, ENST00000430746, ENST00000441239, ENST00000449241, ENST00000464080, ENST00000484982, ENST00000485902, ENST00000486175, ENST00000491269, ENST00000904510, ENST00000904511, ENST00000904512, ENST00000904513, ENST00000904514, ENST00000904515, ENST00000904516, ENST00000904517, ENST00000904518, ENST00000904519, ENST00000904520, ENST00000904521, ENST00000960617, ENST00000960618, ENST00000960619, ENST00000960620, ENST00000960621

RefSeq mRNA: 4 — MANE Select: NM_016210 NM_001171740, NM_001171741, NM_001171743, NM_016210

CCDS: CCDS2829, CCDS54589

Canonical transcript exons

ENST00000357203 — 6 exons

Exon	Start	End
ENSE00000561888	50565466	50565861
ENSE00001520529	50566006	50566094
ENSE00001520530	50567463	50567747
ENSE00003483756	50560917	50561064
ENSE00003528678	50561722	50561747
ENSE00003730056	50558025	50559737

Expression profiles

Bgee: expression breadth ubiquitous, 258 present calls, max score 94.82.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 4.7307 / max 57.4145, expressed in 1368 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
42345	2.8976	1203
42346	1.8332	937

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right hemisphere of cerebellum	UBERON:0014890	94.82	gold quality
cerebellar hemisphere	UBERON:0002245	94.63	gold quality
cerebellar cortex	UBERON:0002129	94.58	gold quality
cerebellum	UBERON:0002037	93.94	gold quality
apex of heart	UBERON:0002098	93.47	gold quality
heart left ventricle	UBERON:0002084	91.14	gold quality
cardiac ventricle	UBERON:0002082	91.08	gold quality
right frontal lobe	UBERON:0002810	89.82	gold quality
prefrontal cortex	UBERON:0000451	89.67	gold quality
right atrium auricular region	UBERON:0006631	89.20	gold quality
heart	UBERON:0000948	88.88	gold quality
hindlimb stylopod muscle	UBERON:0004252	88.62	gold quality
cardiac atrium	UBERON:0002081	88.56	gold quality
inferior olivary complex	UBERON:0002127	88.31	gold quality
cingulate cortex	UBERON:0003027	88.30	gold quality
anterior cingulate cortex	UBERON:0009835	88.28	gold quality
heart right ventricle	UBERON:0002080	88.10	gold quality
caudate nucleus	UBERON:0001873	88.06	gold quality
putamen	UBERON:0001874	87.91	gold quality
nucleus accumbens	UBERON:0001882	87.91	gold quality
frontal cortex	UBERON:0001870	87.81	gold quality
neocortex	UBERON:0001950	87.56	gold quality
Brodmann (1909) area 9	UBERON:0013540	87.50	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	87.46	gold quality
dorsal motor nucleus of vagus nerve	UBERON:0002870	87.45	gold quality
muscle of leg	UBERON:0001383	87.20	gold quality
gastrocnemius	UBERON:0001388	86.91	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	86.77	gold quality
muscle organ	UBERON:0001630	86.63	gold quality
stromal cell of endometrium	CL:0002255	86.62	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-MTAB-9801	yes	7.04
E-MTAB-7303	no	384.24
E-ANND-3	no	2.63

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

75 targeting C3orf18, 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-3689D	100.00	66.14	1181
HSA-MIR-6851-5P	100.00	65.63	1294
HSA-MIR-4510	100.00	66.60	2050
HSA-MIR-6127	100.00	66.76	2188
HSA-MIR-6129	100.00	66.46	2080
HSA-MIR-6130	100.00	66.69	2012
HSA-MIR-6133	100.00	66.48	2064
HSA-MIR-4319	99.76	69.83	2586
HSA-MIR-92A-2-5P	99.75	67.01	2164
HSA-MIR-4306	99.72	70.50	3630
HSA-MIR-1179	99.71	68.70	1040
HSA-MIR-3059-5P	99.70	69.93	2491
HSA-MIR-670-5P	99.67	69.94	1565
HSA-MIR-6887-3P	99.66	67.83	1778
HSA-MIR-4527	99.66	67.43	714
HSA-MIR-6126	99.62	68.09	996
HSA-MIR-6503-5P	99.62	66.96	597
HSA-MIR-1249-5P	99.61	66.55	2049
HSA-MIR-6797-5P	99.61	66.55	2084
HSA-MIR-18A-3P	99.56	65.68	1092
HSA-MIR-4441	99.49	66.56	3216
HSA-MIR-1207-5P	99.49	69.11	2983
HSA-MIR-4316	99.37	65.75	1360
HSA-MIR-155-5P	99.35	70.16	1509
HSA-MIR-5589-3P	99.29	68.30	1443
HSA-MIR-4667-3P	99.26	65.45	1608
HSA-MIR-4291	99.20	68.88	2969
HSA-MIR-10399-5P	99.17	69.87	2610
HSA-MIR-6504-3P	99.17	69.31	2891
HSA-MIR-6734-3P	99.15	66.27	1627

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	C6H3orf18	ENSDARG00000100263
mus_musculus	6430571L13Rik	ENSMUSG00000037977
rattus_norvegicus	C8h3orf18	ENSRNOG00000015718

Paralogs (1): SMIM29 (ENSG00000186577)

Protein

Protein identifiers

Uncharacterized protein C3orf18 — Q9UK00 (reviewed: Q9UK00)

Alternative names: Protein G20

All UniProt accessions (3): Q9UK00, C9IYC4, F8WCC4

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9UK00-1	1	yes
Q9UK00-2	2

RefSeq proteins (4): NP_001165211, NP_001165212, NP_001165214, NP_057294* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR042351	C3orf18-like	Family

UniProt features (7 total): sequence variant 2, chain 1, transmembrane region 1, region of interest 1, compositionally biased region 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9UK00-F1	63.61	0.12

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 70 (showing top): RUTELLA_RESPONSE_TO_CSF2RB_AND_IL4_UP, BLALOCK_ALZHEIMERS_DISEASE_UP, RUTELLA_RESPONSE_TO_HGF_VS_CSF2RB_AND_IL4_DN, PPAR_DR1_Q2, AGCATTA_MIR155, ER_Q6_02, RUTELLA_RESPONSE_TO_HGF_UP, COUP_DR1_Q6, MARTENS_TRETINOIN_RESPONSE_UP, GACAGGG_MIR339, FORTSCHEGGER_PHF8_TARGETS_DN, NOTCH_DN.V1_DN, chr3p21, ASH1L_TARGET_GENES, MIER1_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (1): membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	1

Protein interactions and networks

STRING

754 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
C3orf18	WHR1	P49842	601
C3orf18	ABHD1	Q96SE0	501
C3orf18	TMED1	Q13445	497
C3orf18	FAM3A	P98173	492
C3orf18	TMEM89	A2RUT3	480
C3orf18	DENND1A	Q8TEH3	477
C3orf18	LACTB	P83096	476
C3orf18	WIPF2	Q8TF74	475
C3orf18	MRPL45	Q9BRJ2	474
C3orf18	SYNGR1	O43759	464
C3orf18	UNC45A	Q9H3U1	462
C3orf18	MCFD2	Q8NI22	458
C3orf18	HEATR1	Q9H583	458
C3orf18	EOGT	Q5NDL2	450
C3orf18	C16orf86	Q6ZW13	444

IntAct

5 interactions, top by confidence:

A	B	Type	Score
C3orf18	SPAG9	psi-mi:“MI:0914”(association)	0.530
C3orf18	EXOC5	psi-mi:“MI:0914”(association)	0.350
C3orf18	IPO5	psi-mi:“MI:0914”(association)	0.350
SNRPC	DUSP11	psi-mi:“MI:0914”(association)	0.350

BioGRID (121): C3orf18 (Affinity Capture-RNA), TIMELESS (Affinity Capture-MS), CCDC115 (Affinity Capture-MS), LANCL2 (Affinity Capture-MS), MAPK9 (Affinity Capture-MS), DAK (Affinity Capture-MS), PEX19 (Affinity Capture-MS), INTS1 (Affinity Capture-MS), NCAPG (Affinity Capture-MS), TBC1D9 (Affinity Capture-MS), SACS (Affinity Capture-MS), NCAPD3 (Affinity Capture-MS), IP6K1 (Affinity Capture-MS), EIF2B2 (Affinity Capture-MS), EIF2B4 (Affinity Capture-MS)

ESM2 similar proteins: A0JPB5, A2A699, A5PLA0, A6QPA0, A8MVW0, B0BN44, B4DS77, D3ZZP4, O35451, P04921, P28906, Q06186, Q08DP3, Q08EA8, Q13113, Q1LVN1, Q28270, Q5F3A4, Q5FVQ7, Q5HZE8, Q5R5B8, Q60846, Q640B5, Q64314, Q7TNI2, Q810F0, Q86VZ4, Q8C4Q9, Q8CB67, Q8IUW5, Q8K064, Q8K201, Q8K2J7, Q8NC54, Q8NEA5, Q8R138, Q8TBP5, Q8WWG9, Q96L08, Q99941

Diamond homologs: Q86T20, Q8BGK9, Q8R043, Q9UK00

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	21
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1791 predictions. Top by Δscore:

Variant	Effect	Δscore
3:50560912:CCCA:C	donor_loss	1.0000
3:50560913:CCA:C	donor_loss	1.0000
3:50560914:CA:C	donor_loss	1.0000
3:50560915:ACC:A	donor_loss	1.0000
3:50560916:CCTT:C	donor_loss	1.0000
3:50560920:G:A	donor_gain	1.0000
3:50561060:CCAGC:C	acceptor_gain	1.0000
3:50561061:CAGC:C	acceptor_gain	1.0000
3:50561061:CAGCC:C	acceptor_gain	1.0000
3:50561064:CCT:C	acceptor_loss	1.0000
3:50561065:C:CC	acceptor_gain	1.0000
3:50561065:CTGG:C	acceptor_loss	1.0000
3:50567461:A:AC	donor_gain	1.0000
3:50567462:C:CT	donor_gain	1.0000
3:50567465:AAT:A	donor_gain	1.0000
3:50559733:GTAGT:G	acceptor_gain	0.9900
3:50559734:TAGT:T	acceptor_gain	0.9900
3:50559735:AGTC:A	acceptor_loss	0.9900
3:50559736:GT:G	acceptor_gain	0.9900
3:50559737:TC:T	acceptor_loss	0.9900
3:50559738:C:CC	acceptor_gain	0.9900
3:50559738:CTGC:C	acceptor_loss	0.9900
3:50560944:AGCAG:A	donor_gain	0.9900
3:50561002:T:C	donor_gain	0.9900
3:50561062:AGC:A	acceptor_gain	0.9900
3:50561063:GC:G	acceptor_gain	0.9900
3:50561064:CC:C	acceptor_gain	0.9900
3:50561066:T:C	acceptor_loss	0.9900
3:50561718:TTA:T	donor_loss	0.9900
3:50561721:C:T	donor_loss	0.9900

AlphaMissense

1049 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:50561041:A:G	L95P	0.995
3:50561022:G:C	F101L	0.994
3:50561022:G:T	F101L	0.994
3:50561024:A:G	F101L	0.994
3:50561041:A:T	L95H	0.991
3:50565485:A:T	I72K	0.991
3:50561053:A:G	L91P	0.990
3:50565483:C:G	G73R	0.990
3:50565491:G:T	T70K	0.990
3:50565482:C:T	G73D	0.988
3:50561023:A:C	F101C	0.986
3:50561036:G:A	P97S	0.986
3:50565501:C:G	G67R	0.986
3:50565501:C:T	G67R	0.986
3:50561050:C:G	R92P	0.985
3:50561035:G:T	P97H	0.984
3:50565500:C:T	G67E	0.984
3:50565491:G:C	T70R	0.982
3:50561029:T:C	Y99C	0.980
3:50561030:A:G	Y99H	0.979
3:50561051:G:T	R92S	0.979
3:50559687:A:C	F153L	0.977
3:50559687:A:T	F153L	0.977
3:50559689:A:G	F153L	0.977
3:50561035:G:C	P97R	0.977
3:50561036:G:T	P97T	0.977
3:50561038:A:G	M96T	0.977
3:50565485:A:C	I72R	0.977
3:50561044:T:G	Q94P	0.976
3:50561023:A:G	F101S	0.974

dbSNP variants (sampled 300 via entrez): RS1000108966 (3:50572428 C>A,T), RS1000381217 (3:50573014 C>T), RS1000544415 (3:50572112 C>T), RS1000657270 (3:50567037 G>A), RS1000710626 (3:50567526 C>G,T), RS1001051982 (3:50568400 G>A), RS1001118204 (3:50561902 C>T), RS1001508421 (3:50567548 G>A,T), RS1001518557 (3:50570984 G>A,C), RS1001548211 (3:50561558 G>A), RS1001575353 (3:50560635 C>T), RS1001626418 (3:50567809 G>A), RS1002019284 (3:50560723 C>T), RS1002192827 (3:50574126 G>A), RS1002477238 (3:50568865 G>A)

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

7 associations (top):

Study	Trait	p-value
GCST005860_2	Cholangiocarcinoma in primary sclerosing cholangitis (time to event)	4.000000e-06
GCST007483_9	Waist-to-hip ratio adjusted for BMI (additive genetic model)	2.000000e-07
GCST007487_1	Waist-to-hip ratio adjusted for BMI (additive genetic model)	6.000000e-07
GCST008399_4	Cocaine dependence	7.000000e-06
GCST008843_1	Depressive symptom (appetite changes) (binary trait)	9.000000e-09
GCST008848_2	Depressive symptoms (sum-score)	1.000000e-09
GCST008849_3	Depressive symptoms (binary sum-score)	1.000000e-10

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0007788	BMI-adjusted waist-hip ratio
EFO:0007006	depressive symptom measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

27 total (human), top 27 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
GSK-J4	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
perfluorooctanoic acid	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	decreases expression	1
perfluoro-n-nonanoic acid	decreases expression	1
2-palmitoylglycerol	increases expression	1
perfluorohexanesulfonic acid	decreases expression	1
abrine	decreases expression	1
jinfukang	affects cotreatment, increases expression	1
(+)-JQ1 compound	decreases expression	1
Temozolomide	decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Amiodarone	increases expression	1
Benzo(a)pyrene	increases methylation	1
Cisplatin	affects cotreatment, increases expression	1
Diethylhexyl Phthalate	decreases expression	1
Diuron	decreases expression	1
Doxorubicin	decreases expression	1
Hydrogen Peroxide	affects expression	1
Tobacco Smoke Pollution	decreases expression	1
Valproic Acid	decreases methylation	1
Aflatoxin B1	decreases methylation	1
Antirheumatic Agents	increases expression	1
Copper Sulfate	decreases expression	1
Acrylamide	decreases expression	1
Particulate Matter	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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