C1orf54

Summary

C1orf54 (chromosome 1 open reading frame 54, HGNC:26258) is a protein-coding gene on chromosome 1q21.2, encoding Uncharacterized protein C1orf54 (Q8WWF1).

Predicted to act upstream of or within epithelial cell proliferation involved in renal tubule morphogenesis; phosphatidylinositol 3-kinase/protein kinase B signal transduction; and response to wounding. Predicted to be located in extracellular region.

Source: NCBI Gene 79630 — RefSeq curated summary.

At a glance

• GWAS associations: 14
• Clinical variants (ClinVar): 8 total
• MANE Select transcript: NM_024579

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26258
Approved symbol	C1orf54
Name	chromosome 1 open reading frame 54
Location	1q21.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ23221
Ensembl gene	ENSG00000118292
Ensembl biotype	protein_coding
Entrez	79630

Gene structure

Transcript identifiers

Ensembl transcripts: 27 — 27 protein_coding

ENST00000369098, ENST00000369099, ENST00000369102, ENST00000877303, ENST00000877304, ENST00000877305, ENST00000877306, ENST00000877307, ENST00000877308, ENST00000877309, ENST00000877310, ENST00000877311, ENST00000877312, ENST00000877313, ENST00000877314, ENST00000913716, ENST00000913717, ENST00000913718, ENST00000913719, ENST00000913720, ENST00000953964, ENST00000953965, ENST00000953966, ENST00000953967, ENST00000953968, ENST00000953969, ENST00000953970

RefSeq mRNA: 5 — MANE Select: NM_024579 NM_001301039, NM_001301040, NM_001301041, NM_001301042, NM_024579

CCDS: CCDS72905, CCDS948

Canonical transcript exons

ENST00000369099 — 6 exons

Exon	Start	End
ENSE00000787762	150275741	150275799
ENSE00000787763	150274087	150274170
ENSE00000797129	150279643	150279741
ENSE00000797130	150276522	150276632
ENSE00001448807	150280835	150280916
ENSE00001895063	150272790	150272863

Expression profiles

Bgee: expression breadth ubiquitous, 267 present calls, max score 97.85.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 10.2292 / max 162.1829, expressed in 1140 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
5087	8.1329	1101
5086	2.0963	809

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
periodontal ligament	UBERON:0008266	97.85	gold quality
descending thoracic aorta	UBERON:0002345	97.69	gold quality
thoracic aorta	UBERON:0001515	97.29	gold quality
ascending aorta	UBERON:0001496	97.28	gold quality
aorta	UBERON:0000947	97.09	gold quality
right coronary artery	UBERON:0001625	97.06	gold quality
tibial artery	UBERON:0007610	97.00	gold quality
popliteal artery	UBERON:0002250	96.99	gold quality
left coronary artery	UBERON:0001626	96.34	gold quality
coronary artery	UBERON:0001621	96.22	gold quality
vena cava	UBERON:0004087	95.95	gold quality
left uterine tube	UBERON:0001303	95.81	gold quality
saphenous vein	UBERON:0007318	95.81	gold quality
mucosa of stomach	UBERON:0001199	95.18	gold quality
gall bladder	UBERON:0002110	94.81	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	94.50	gold quality
smooth muscle tissue	UBERON:0001135	94.23	gold quality
spleen	UBERON:0002106	94.18	gold quality
stromal cell of endometrium	CL:0002255	93.98	gold quality
lower esophagus muscularis layer	UBERON:0035833	93.87	gold quality
lymph node	UBERON:0000029	93.81	gold quality
lower esophagus	UBERON:0013473	93.80	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	93.67	gold quality
putamen	UBERON:0001874	93.46	gold quality
seminal vesicle	UBERON:0000998	93.44	gold quality
caudate nucleus	UBERON:0001873	93.40	gold quality
superficial temporal artery	UBERON:0001614	93.38	gold quality
peritoneum	UBERON:0002358	93.31	gold quality
omental fat pad	UBERON:0010414	93.30	gold quality
spinal cord	UBERON:0002240	93.02	gold quality

Single-cell (SCXA)

Detected in 17 experiment(s), a significant marker in 17.

Experiment	Marker?	Max mean expression
E-MTAB-8207	yes	2671.50
E-GEOD-89232	yes	2391.77
E-HCAD-13	yes	1070.17
E-MTAB-6701	yes	1070.08
E-HCAD-1	yes	870.97
E-HCAD-32	yes	686.97
E-MTAB-6678	yes	485.56
E-HCAD-11	yes	39.36
E-MTAB-8410	yes	28.32
E-MTAB-10553	yes	26.03
E-CURD-112	yes	16.44
E-CURD-88	yes	10.08
E-MTAB-10042	yes	8.94
E-GEOD-83139	yes	7.46
E-GEOD-84465	yes	6.62

Regulation

Is transcription factor: no

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	BC028528	ENSMUSG00000038543
rattus_norvegicus	C2h1orf54	ENSRNOG00000059750

Protein

Protein identifiers

Uncharacterized protein C1orf54 — Q8WWF1 (reviewed: Q8WWF1)

All UniProt accessions (2): Q8WWF1, Q5TB16

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Secreted.

RefSeq proteins (5): NP_001287968, NP_001287969, NP_001287970, NP_001287971, NP_078855* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR027957	DUF4634	Family

Pfam: PF15465

UniProt features (3 total): signal peptide 1, chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8WWF1-F1	66.41	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 175 (showing top): WALLACE_PROSTATE_CANCER_RACE_UP, BHATI_G2M_ARREST_BY_2METHOXYESTRADIOL_DN, WIELAND_UP_BY_HBV_INFECTION, MARTINEZ_RB1_TARGETS_UP, GOBP_PHOSPHATIDYLINOSITOL_3_KINASE_PROTEIN_KINASE_B_SIGNAL_TRANSDUCTION, KINSEY_TARGETS_OF_EWSR1_FLII_FUSION_DN, CCCNNGGGAR_OLF1_01, ACEVEDO_LIVER_CANCER_UP, MARTINEZ_RB1_AND_TP53_TARGETS_UP, VALK_AML_CLUSTER_16, chr1q21, SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_UP, MULLIGHAN_MLL_SIGNATURE_1_UP, RHEIN_ALL_GLUCOCORTICOID_THERAPY_DN, GAZDA_DIAMOND_BLACKFAN_ANEMIA_ERYTHROID_DN

GO Biological Process (3): response to wounding (GO:0009611), phosphatidylinositol 3-kinase/protein kinase B signal transduction (GO:0043491), epithelial cell proliferation involved in renal tubule morphogenesis (GO:2001013)

GO Molecular Function (0):

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

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
response to stress	1
intracellular signaling cassette	1
epithelial cell proliferation	1
renal tubule morphogenesis	1
cellular anatomical structure	1

Protein interactions and networks

STRING

276 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
C1orf54	LRRC47	Q8N1G4	465
C1orf54	RBMS2	Q15434	414
C1orf54	CLEC9A	Q6UXN8	394
C1orf54	SLC61A1	Q6N075	370
C1orf54	XTBD1	Q96HQ2	356
C1orf54	CLEC10A	Q8IUN9	350
C1orf54	SUCLG2	Q96I99	337
C1orf54	MPPE1	Q53F39	322
C1orf54	MAD1L1	Q9Y6D9	316
C1orf54	FCER1A	P12319	312
C1orf54	NSMCE4A	Q9NXX6	307
C1orf54	ANKDD1A	Q495B1	306
C1orf54	ZCRB1	Q8TBF4	285
C1orf54	COMMD5	Q9GZQ3	284
C1orf54	TM4SF19	Q96DZ7	273

IntAct

4 interactions, top by confidence:

A	B	Type	Score
C1orf54	EXTL3	psi-mi:“MI:0914”(association)	0.530
C1orf54	AGRN	psi-mi:“MI:0914”(association)	0.350
C1orf54	QSOX1	psi-mi:“MI:0914”(association)	0.350

BioGRID (166): PLXNA3 (Affinity Capture-MS), SCARB1 (Affinity Capture-MS), LRRC24 (Affinity Capture-MS), TMEM62 (Affinity Capture-MS), ERO1LB (Affinity Capture-MS), MAN2B2 (Affinity Capture-MS), ST3GAL6 (Affinity Capture-MS), LRFN3 (Affinity Capture-MS), GLB1L (Affinity Capture-MS), VWA1 (Affinity Capture-MS), B4GALT7 (Affinity Capture-MS), TENM3 (Affinity Capture-MS), GLT8D2 (Affinity Capture-MS), TMEM132A (Affinity Capture-MS), LRIG1 (Affinity Capture-MS)

ESM2 similar proteins: A0A023FF81, A0A0K1YW63, A0A146B485, A0A146B5A4, A0A158RFT4, A0A8U0LTT9, A0A8U0LU66, A7A108, B3EWF6, B3LT72, C5DMZ6, C5DVG0, C7GQS7, C8ZD75, E2J6T4, I1VC85, O36359, O57166, O61704, P01136, P02852, P0DOP9, P0DOQ0, P0DQV0, P20494, P22334, P34671, P50605, P61110, P81694, Q03345, Q08045, Q1AGV7, Q27384, Q27913, Q54DH5, Q5WRS0, Q6BNN2, Q776B5, Q7YWA6

Diamond homologs: Q148C7, Q8R2K8, Q8WWF1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

8 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

1461 predictions. Top by Δscore:

Variant	Effect	Δscore
1:150268126:CC:C	acceptor_gain	1.0000
1:150268127:CC:C	acceptor_gain	1.0000
1:150268779:A:T	donor_gain	1.0000
1:150272796:C:G	acceptor_gain	1.0000
1:150272798:GC:G	acceptor_gain	1.0000
1:150272798:GCA:G	acceptor_gain	1.0000
1:150272860:CTGGG:C	donor_loss	1.0000
1:150272862:GG:G	donor_gain	1.0000
1:150272863:GG:G	donor_gain	1.0000
1:150272864:G:C	donor_loss	1.0000
1:150272864:G:GG	donor_gain	1.0000
1:150272865:T:A	donor_loss	1.0000
1:150268123:ATGCC:A	acceptor_gain	0.9900
1:150268124:TGCC:T	acceptor_gain	0.9900
1:150268128:C:CC	acceptor_gain	0.9900
1:150268128:C:T	acceptor_gain	0.9900
1:150268128:CTGAG:C	acceptor_loss	0.9900
1:150268129:T:A	acceptor_loss	0.9900
1:150268696:AC:A	donor_gain	0.9900
1:150268697:CC:C	donor_gain	0.9900
1:150269114:G:A	donor_gain	0.9900
1:150269157:G:GT	donor_gain	0.9900
1:150272794:CACA:C	acceptor_loss	0.9900
1:150272795:A:AG	acceptor_gain	0.9900
1:150272795:ACAGC:A	acceptor_loss	0.9900
1:150272797:A:AG	acceptor_gain	0.9900
1:150272797:A:T	acceptor_loss	0.9900
1:150272798:G:GG	acceptor_gain	0.9900
1:150272798:GCAA:G	acceptor_gain	0.9900
1:150272798:GCAAT:G	acceptor_gain	0.9900

AlphaMissense

861 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:150275758:T:C	F50L	0.968
1:150275760:C:A	F50L	0.968
1:150275760:C:G	F50L	0.968
1:150275779:T:C	F57L	0.937
1:150275781:T:A	F57L	0.937
1:150275781:T:G	F57L	0.937
1:150275759:T:C	F50S	0.934
1:150275759:T:G	F50C	0.931
1:150275780:T:G	F57C	0.915
1:150272846:C:A	A10D	0.892
1:150274156:T:A	V39D	0.891
1:150272837:C:A	A7D	0.851
1:150272863:G:A	G16R	0.846
1:150272863:G:C	G16R	0.846
1:150274162:C:A	P41H	0.836
1:150275780:T:C	F57S	0.835
1:150275765:T:A	I52N	0.808
1:150275767:G:C	D53H	0.804
1:150275768:A:T	D53V	0.800
1:150272849:T:A	V11E	0.795
1:150274087:G:T	G16V	0.786
1:150275769:T:A	D53E	0.781
1:150275769:T:G	D53E	0.781
1:150274156:T:G	V39G	0.774
1:150274087:G:A	G16E	0.764
1:150274162:C:G	P41R	0.764
1:150272852:C:G	P12R	0.759
1:150275765:T:G	I52S	0.746
1:150272858:T:A	I14N	0.743
1:150274161:C:A	P41T	0.738

dbSNP variants (sampled 300 via entrez): RS1000017680 (1:150268281 G>A,C), RS1000163033 (1:150280513 G>A), RS1000336066 (1:150273175 G>A), RS1001581857 (1:150279212 C>T), RS1002580748 (1:150277698 G>T), RS1002712264 (1:150270820 C>A,T), RS1002775812 (1:150278045 C>T), RS1003787393 (1:150276393 G>A), RS1004120862 (1:150269354 A>T), RS1004459059 (1:150266916 G>A), RS1004493200 (1:150281127 C>A), RS1005082475 (1:150279579 G>A), RS1005145699 (1:150272205 A>G), RS1005239208 (1:150272052 A>C), RS1005420218 (1:150279140 G>A,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

14 associations (top):

Study	Trait	p-value
GCST002539_32	Schizophrenia	4.000000e-10
GCST005038_31	Allergic disease (asthma, hay fever or eczema)	1.000000e-09
GCST007430_18	Peak expiratory flow	2.000000e-11
GCST007431_111	Lung function (FEV1/FVC)	3.000000e-06
GCST008103_32	Bipolar disorder	5.000000e-08
GCST010696_11	Cortical thickness (min-P)	2.000000e-23
GCST010697_17	Cortical surface area (min-P)	9.000000e-09
GCST010698_23	Subcortical volume (min-P)	2.000000e-08
GCST010699_48	Brain morphology (min-P)	3.000000e-08
GCST010700_28	Cortical thickness (MOSTest)	8.000000e-38
GCST010701_113	Cortical surface area (MOSTest)	9.000000e-12
GCST010702_126	Subcortical volume (MOSTest)	4.000000e-09
GCST010703_244	Brain morphology (MOSTest)	9.000000e-12
GCST010726_82	Periventricular white matter hyperintensities	7.000000e-06

EFO canonical traits (5, from GWAS)

EFO ID	Trait name
EFO:0009718	peak expiratory flow
EFO:0004713	FEV/FVC ratio
EFO:0004346	neuroimaging measurement
EFO:0004840	cortical thickness
EFO:0005665	white matter hyperintensity measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	decreases methylation, affects cotreatment, decreases expression, affects expression	8
Benzo(a)pyrene	decreases expression, increases methylation	2
Silicon Dioxide	increases expression, decreases expression	2
Cyclosporine	increases expression	2
bisphenol F	affects cotreatment, increases expression	1
testosterone enanthate	affects expression	1
propionaldehyde	increases expression	1
bisphenol A	affects cotreatment, increases expression	1
lead acetate	decreases expression	1
kojic acid	increases expression	1
beta-lapachone	increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
sodium arsenite	increases expression	1
pentabromodiphenyl ether	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
abrine	increases expression	1
2,2’,4,4’-tetrabromodiphenyl ether	increases expression	1
2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amide	decreases reaction, increases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
Temozolomide	decreases expression	1
Pioglitazone	decreases expression	1
Decitabine	affects expression	1
Sunitinib	decreases expression	1
Vehicle Emissions	decreases reaction, increases expression	1
Cadmium	decreases expression	1
Cisplatin	affects expression	1
Dexamethasone	affects cotreatment, increases expression	1
Diuron	decreases expression	1
Drugs, Chinese Herbal	increases expression	1
Indomethacin	affects cotreatment, increases expression	1

Clinical trials (associated diseases)

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