C1orf53

Summary

C1orf53 (chromosome 1 open reading frame 53, HGNC:30003) is a protein-coding gene on chromosome 1q31.3, encoding Uncharacterized protein C1orf53 (Q5VUE5).

Located in mitochondrion.

Source: NCBI Gene 388722 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 4 total
• MANE Select transcript: NM_001024594

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30003
Approved symbol	C1orf53
Name	chromosome 1 open reading frame 53
Location	1q31.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000203724
Ensembl biotype	protein_coding
Entrez	388722

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 3 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000367393, ENST00000436652, ENST00000542800, ENST00000905842

RefSeq mRNA: 1 — MANE Select: NM_001024594 NM_001024594

CCDS: CCDS44290

Canonical transcript exons

ENST00000367393 — 3 exons

Exon	Start	End
ENSE00001444417	197902630	197902913
ENSE00003516451	197905796	197905897
ENSE00003845018	197907149	197907362

Expression profiles

Bgee: expression breadth ubiquitous, 198 present calls, max score 91.90.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 6.3477 / max 70.0069, expressed in 1582 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
7525	5.7837	1544
7527	0.5201	324
7526	0.0440	7

Top tissues by expression

238 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	91.90	gold quality
endothelial cell	CL:0000115	89.17	gold quality
right lobe of liver	UBERON:0001114	84.68	gold quality
right adrenal gland cortex	UBERON:0035827	83.04	gold quality
oocyte	CL:0000023	82.88	gold quality
adrenal tissue	UBERON:0018303	82.86	gold quality
right adrenal gland	UBERON:0001233	82.70	gold quality
left adrenal gland	UBERON:0001234	81.95	gold quality
germinal epithelium of ovary	UBERON:0001304	81.93	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	81.60	gold quality
left adrenal gland cortex	UBERON:0035825	81.49	gold quality
adrenal cortex	UBERON:0001235	80.96	gold quality
liver	UBERON:0002107	80.48	gold quality
pigmented layer of retina	UBERON:0001782	80.16	gold quality
secondary oocyte	CL:0000655	80.05	gold quality
adrenal gland	UBERON:0002369	79.97	gold quality
amygdala	UBERON:0001876	78.37	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	78.08	gold quality
anterior cingulate cortex	UBERON:0009835	77.73	gold quality
heart left ventricle	UBERON:0002084	77.43	gold quality
mucosa of transverse colon	UBERON:0004991	77.38	gold quality
right atrium auricular region	UBERON:0006631	77.19	gold quality
adenohypophysis	UBERON:0002196	76.96	gold quality
cardiac ventricle	UBERON:0002082	76.87	gold quality
cardiac atrium	UBERON:0002081	76.68	gold quality
Brodmann (1909) area 9	UBERON:0013540	76.39	gold quality
stromal cell of endometrium	CL:0002255	76.38	gold quality
hindlimb stylopod muscle	UBERON:0004252	76.23	gold quality
metanephros	UBERON:0000081	75.83	gold quality
hypothalamus	UBERON:0001898	75.77	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	7.36

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

27 targeting C1orf53, 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-1277-5P	100.00	73.95	5056
HSA-MIR-3924	100.00	72.09	2394
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-1297	99.91	73.41	3162
HSA-MIR-579-3P	99.86	71.66	3628
HSA-MIR-664B-3P	99.84	71.65	3590
HSA-MIR-26A-5P	99.78	73.52	2303
HSA-MIR-26B-5P	99.78	73.51	2305
HSA-MIR-4255	99.72	67.70	1541
HSA-MIR-4465	99.71	72.56	2096
HSA-MIR-4677-5P	99.70	70.09	1940
HSA-MIR-651-5P	99.64	68.49	1104
HSA-MIR-4756-3P	99.62	66.30	1319
HSA-MIR-7844-5P	99.55	68.56	1428
HSA-MIR-5584-5P	99.49	68.22	2814
HSA-MIR-208A-5P	99.42	70.83	1913
HSA-MIR-208B-5P	99.42	70.83	1952
HSA-MIR-2116-5P	99.32	69.34	1273
HSA-MIR-4260	98.78	65.37	848
HSA-MIR-9500	98.62	66.54	1845
HSA-MIR-124-5P	98.11	67.65	1095
HSA-MIR-3159	97.94	66.79	1098
HSA-MIR-22-5P	97.67	68.92	1355
HSA-MIR-5586-5P	96.29	68.02	685
HSA-MIR-6750-5P	93.94	66.68	797
HSA-MIR-6822-5P	93.94	66.34	812

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	C22H1orf53	ENSDARG00000071439
mus_musculus	2310009B15Rik	ENSMUSG00000079283
rattus_norvegicus	C13h1orf53	ENSRNOG00000043374
caenorhabditis_elegans		WBGENE00018475

Paralogs (1): MRPL14 (ENSG00000180992)

Protein

Protein identifiers

Uncharacterized protein C1orf53 — Q5VUE5 (reviewed: Q5VUE5)

All UniProt accessions (2): Q5VUE5, H7C0U6

UniProt curated annotations — full annotation on UniProt →

Tissue specificity. Expressed in retina and retinoblastoma.

RefSeq proteins (1): NP_001019765* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR040807	DUF5522	Family

Pfam: PF17653

UniProt features (2 total): chain 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5VUE5-F1	73.54	0.30

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 (1): 67

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 64 (showing top): GOZGIT_ESR1_TARGETS_DN, SENESE_HDAC1_AND_HDAC2_TARGETS_DN, WEBER_METHYLATED_IN_COLON_CANCER, CHIANG_LIVER_CANCER_SUBCLASS_CTNNB1_UP, ZHAN_MULTIPLE_MYELOMA_CD2_DN, GEORGES_TARGETS_OF_MIR192_AND_MIR215, CHEN_LIVER_METABOLISM_QTL_CIS, PEDRIOLI_MIR31_TARGETS_UP, CHAF1B_TARGET_GENES, FEV_TARGET_GENES, KAT5_TARGET_GENES, GSE10240_CTRL_VS_IL17_AND_IL22_STIM_PRIMARY_BRONCHIAL_EPITHELIAL_CELLS_UP, ZNF407_TARGET_GENES, ZNF610_TARGET_GENES, ZNF618_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (1): mitochondrion (GO:0005739)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cytoplasm	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

132 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
C1orf53	C21orf140	B9A014	591
C1orf53	DENND1B	Q6P3S1	522
C1orf53	TMA16	Q96EY4	475
C1orf53	TEX29	Q8N6K0	432
C1orf53	HIGD1C	A8MV81	400
C1orf53	BRIX1	Q8TDN6	393
C1orf53	FARSB	Q9NSD9	384
C1orf53	ZNF326	Q5BKZ1	384
C1orf53	ZNF394	Q53GI3	371
C1orf53	BTBD10	Q9BSF8	367
C1orf53	A0A0B4J2G0	A0A0B4J2G0	349
C1orf53	BEX4	Q9NWD9	349
C1orf53	BTBD3	Q9Y2F9	321
C1orf53	B3GALT2	O43825	313
C1orf53	ATP6V1G3	Q96LB4	308

IntAct

0 interactions, top by confidence:

BioGRID (2): DCXR (Co-fractionation), C1orf53 (Co-fractionation)

ESM2 similar proteins: A2A8U2, A6H773, A6QPI4, D4A6L0, E1BBQ2, O60232, P54098, Q05B67, Q08BI9, Q148E1, Q2KI76, Q2KJ58, Q2NL34, Q32Q90, Q4R4I0, Q5C9Z4, Q5RE99, Q5SNT2, Q5T6X4, Q5T848, Q5VUE5, Q5XIJ4, Q5ZLJ4, Q6DVA0, Q6P3B9, Q7T076, Q80YR4, Q86UK7, Q8C419, Q8CEG5, Q8IYL2, Q8N0V3, Q8NC56, Q8TBN0, Q8VDV3, Q8VE22, Q8VHV8, Q921N7, Q96IL0, Q96ND0

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

408 predictions. Top by Δscore:

Variant	Effect	Δscore
1:197905784:A:AG	acceptor_gain	1.0000
1:197905785:T:G	acceptor_gain	1.0000
1:197905789:A:AG	acceptor_gain	1.0000
1:197905790:C:G	acceptor_gain	1.0000
1:197905791:TTCA:T	acceptor_loss	1.0000
1:197905793:CAGGC:C	acceptor_loss	1.0000
1:197905794:A:AG	acceptor_gain	1.0000
1:197905794:A:AT	acceptor_loss	1.0000
1:197905794:AG:A	acceptor_gain	1.0000
1:197905794:AGGCT:A	acceptor_gain	1.0000
1:197905795:G:GC	acceptor_gain	1.0000
1:197905795:GG:G	acceptor_gain	1.0000
1:197905795:GGCT:G	acceptor_gain	1.0000
1:197905795:GGCTG:G	acceptor_gain	1.0000
1:197905898:G:GG	donor_gain	1.0000
1:197905784:ATT:A	acceptor_gain	0.9900
1:197905786:T:TA	acceptor_gain	0.9900
1:197905795:GGC:G	acceptor_gain	0.9900
1:197905893:GACAT:G	donor_gain	0.9900
1:197905896:ATGT:A	donor_loss	0.9900
1:197905897:TGT:T	donor_loss	0.9900
1:197905898:G:C	donor_loss	0.9900
1:197905899:T:TA	donor_loss	0.9900
1:197905900:GAGTA:G	donor_loss	0.9900
1:197905901:AGTAG:A	donor_loss	0.9900
1:197905902:G:C	donor_loss	0.9900
1:197907147:A:AG	acceptor_gain	0.9900
1:197907148:G:GG	acceptor_gain	0.9900
1:197907148:GT:G	acceptor_gain	0.9900
1:197903113:GTCT:G	donor_gain	0.9800

AlphaMissense

921 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:197907209:T:C	F143L	0.986
1:197907211:T:A	F143L	0.986
1:197907211:T:G	F143L	0.986
1:197907149:T:C	C123R	0.983
1:197905897:T:A	H122Q	0.982
1:197905897:T:G	H122Q	0.982
1:197905893:G:C	R121T	0.981
1:197905894:A:C	R121S	0.980
1:197905894:A:T	R121S	0.980
1:197907149:T:A	C123S	0.979
1:197907150:G:C	C123S	0.979
1:197907197:T:C	F139L	0.979
1:197907199:C:A	F139L	0.979
1:197907199:C:G	F139L	0.979
1:197905874:T:A	C115S	0.974
1:197905875:G:C	C115S	0.974
1:197907171:T:A	V130D	0.972
1:197905874:T:C	C115R	0.969
1:197907150:G:A	C123Y	0.969
1:197905856:C:G	H109D	0.966
1:197907202:T:A	N140K	0.964
1:197907202:T:G	N140K	0.964
1:197907151:T:G	C123W	0.962
1:197905893:G:T	R121I	0.960
1:197905895:C:G	H122D	0.959
1:197907150:G:T	C123F	0.958
1:197905889:T:C	C120R	0.956
1:197905892:A:G	R121G	0.956
1:197905896:A:G	H122R	0.953
1:197905839:T:A	V103E	0.952

dbSNP variants (sampled 300 via entrez): RS1000414344 (1:197904806 A>C), RS1000575352 (1:197902957 G>A,C,T), RS1001201315 (1:197904378 A>C), RS1002184663 (1:197904915 AC>A), RS1002781814 (1:197906738 CT>C), RS1002928927 (1:197902846 C>G,T), RS1003250178 (1:197904501 GT>G,GTT), RS1003599690 (1:197902576 C>A,G,T), RS1004136254 (1:197900962 CTG>C), RS1004317525 (1:197907500 A>T), RS1004365375 (1:197905668 C>A,T), RS1004671823 (1:197905356 G>A), RS1005254293 (1:197902202 GA>G), RS1005895321 (1:197903643 C>T), RS1006009507 (1:197904039 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

3 associations (top):

Study	Trait	p-value
GCST001725_38	Inflammatory bowel disease	8.000000e-13
GCST007830_4	Anti-thyroid peroxidase (TPOAb) levels in Hashimoto’s thyroiditis	3.000000e-06
GCST012033_3	Sleep (1/3-day periodicity)	2.000000e-08

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, increases expression, affects cotreatment, decreases expression	6
trichostatin A	affects cotreatment, decreases expression	3
Cyclosporine	decreases expression, increases expression	3
entinostat	decreases expression, affects cotreatment	2
Panobinostat	decreases expression, affects cotreatment	2
Benzo(a)pyrene	decreases expression, affects methylation	2
methylmercuric chloride	decreases expression	1
bisphenol A	decreases expression	1
sulforaphane	decreases expression	1
sodium arsenite	decreases expression	1
perfluorooctanoic acid	increases expression	1
K 7174	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression, increases expression	1
ICG 001	increases expression	1
dorsomorphin	affects cotreatment, decreases expression, increases expression	1
jinfukang	increases expression	1
Decitabine	affects expression	1
Sunitinib	increases expression	1
Zoledronic Acid	decreases expression	1
Air Pollutants	increases abundance, decreases expression	1
Atrazine	decreases expression	1
Cisplatin	affects expression	1
Mercuric Chloride	affects cotreatment, increases expression	1
Thimerosal	increases expression	1
Thiram	decreases expression	1
Triclosan	increases expression	1
Aflatoxin B1	decreases methylation	1
Cadmium Chloride	decreases expression	1
Lactic Acid	increases expression	1
Genistein	decreases expression	1

Clinical trials (associated diseases)

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