C10orf53

Summary

C10orf53 (chromosome 10 open reading frame 53, HGNC:27421) is a protein-coding gene on chromosome 10q11.23, encoding UPF0728 protein C10orf53 (Q8N6V4).

At a glance

• Clinical variants (ClinVar): 6 total
• MANE Select transcript: NM_001042427

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:27421
Approved symbol	C10orf53
Name	chromosome 10 open reading frame 53
Location	10q11.23
Locus type	gene with protein product
Status	Approved
Aliases	Em:AC069546.1
Ensembl gene	ENSG00000178645
Ensembl biotype	protein_coding
Entrez	282966

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000374111, ENST00000374112, ENST00000374113

RefSeq mRNA: 2 — MANE Select: NM_001042427 NM_001042427, NM_182554

CCDS: CCDS31202, CCDS41521

Canonical transcript exons

ENST00000374111 — 3 exons

Exon	Start	End
ENSE00001385483	49693774	49693893
ENSE00001462500	49694538	49697532
ENSE00001462503	49679651	49679794

Expression profiles

Bgee: expression breadth broad, 29 present calls, max score 94.84.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1231 / max 107.3582, expressed in 14 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
104898	0.1231	14

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	94.84	gold quality
left testis	UBERON:0004533	79.29	gold quality
adult organism	UBERON:0007023	78.88	gold quality
testis	UBERON:0000473	76.98	gold quality
right testis	UBERON:0004534	76.86	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	74.29	gold quality
parotid gland	UBERON:0001831	63.11	gold quality
myocardium	UBERON:0002349	60.00	gold quality
tibialis anterior	UBERON:0001385	59.59	silver quality
nasal cavity epithelium	UBERON:0005384	59.53	gold quality
deltoid	UBERON:0001476	58.67	gold quality
biceps brachii	UBERON:0001507	57.35	gold quality
buccal mucosa cell	CL:0002336	56.53	gold quality
gingival epithelium	UBERON:0001949	55.98	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	55.77	gold quality
cardiac muscle of right atrium	UBERON:0003379	54.94	gold quality
gingiva	UBERON:0001828	54.90	gold quality
lateral globus pallidus	UBERON:0002476	54.36	gold quality
left ventricle myocardium	UBERON:0006566	54.23	gold quality
kidney epithelium	UBERON:0004819	53.93	gold quality
heart right ventricle	UBERON:0002080	53.72	gold quality
cartilage tissue	UBERON:0002418	53.71	gold quality
upper arm skin	UBERON:0004263	53.52	gold quality
epithelial cell of pancreas	CL:0000083	53.23	gold quality
quadriceps femoris	UBERON:0001377	52.78	gold quality
colonic mucosa	UBERON:0000317	52.77	gold quality
mucosa of sigmoid colon	UBERON:0004993	52.75	gold quality
substantia nigra pars reticulata	UBERON:0001966	52.46	gold quality
vastus lateralis	UBERON:0001379	50.90	gold quality
trabecular bone tissue	UBERON:0002483	50.78	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.45

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

9 targeting C10orf53, 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-188-3P	100.00	68.76	1240
HSA-MIR-4648	99.91	67.00	710
HSA-MIR-1299	99.77	71.24	2389
HSA-MIR-3175	99.65	66.30	2031
HSA-MIR-676-5P	98.49	68.87	1492
HSA-MIR-1302	97.92	67.27	844
HSA-MIR-4298	97.26	66.59	765
HSA-MIR-602	97.09	61.68	156
HSA-MIR-6771-5P	86.50	65.30	81

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	C13H10orf53	ENSDARG00000069363
mus_musculus	1700024G13Rik	ENSMUSG00000072473
rattus_norvegicus	C16h10orf53	ENSRNOG00000039749

Protein

Protein identifiers

UPF0728 protein C10orf53 — Q8N6V4 (reviewed: Q8N6V4)

All UniProt accessions (1): Q8N6V4

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the UPF0728 family.

Isoforms (4)

UniProt ID	Names	Canonical?
Q8N6V4-1	1	yes
Q8N6V4-2	2
Q8N6V4-3	3
Q8N6V4-4	4

RefSeq proteins (2): NP_001035892, NP_872360 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR027885	UPF0728	Family

Pfam: PF15092

UniProt features (5 total): splice variant 3, chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N6V4-F1	93.87	0.89

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 22 (showing top): CMYB_01, EFC_Q6, RFX1_01, PR_Q2, HSF1_01, ZNF257_TARGET_GENES, ZNF512_TARGET_GENES, ZNF618_TARGET_GENES, ZNF766_TARGET_GENES, MIR4648, GSE15659_CD45RA_NEG_CD4_TCELL_VS_ACTIVATED_TREG_UP, GSE15659_RESTING_TREG_VS_NONSUPPRESSIVE_TCELL_UP, GSE15659_NONSUPPRESSIVE_TCELL_VS_ACTIVATED_TREG_UP, MYOCD_TARGET_GENES, GSE18791_UNSTIM_VS_NEWCATSLE_VIRUS_DC_2H_UP

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

204 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
C10orf53	C10orf120	Q5SQS8	607
C10orf53	CCDC172	P0C7W6	596
C10orf53	SPMIP4	Q8N865	571
C10orf53	PCMTD1	Q96MG8	519
C10orf53	ST18	O60284	518
C10orf53	EEIG1	Q5T9C2	507
C10orf53	C7orf57	Q8NEG2	506
C10orf53	DPM2	O94777	469
C10orf53	EPDR1	Q9UM22	452
C10orf53	PHETA2	Q6ICB4	447
C10orf53	PLEKHA7	Q6IQ23	420
C10orf53	NHSL1	Q5SYE7	398
C10orf53	RERGL	Q9H628	358
C10orf53	FERMT2	Q96AC1	310
C10orf53	CC2D1A	Q6P1N0	306

IntAct

4 interactions, top by confidence:

A	B	Type	Score
C10orf53	SPTB	psi-mi:“MI:0915”(physical association)	0.400
C10orf53	CST4	psi-mi:“MI:0914”(association)	0.350
C10orf53	NIF3L1	psi-mi:“MI:0914”(association)	0.350

BioGRID (12): SPTB (Affinity Capture-MS), ZG16B (Affinity Capture-MS), DSCC1 (Affinity Capture-MS), UXT (Affinity Capture-MS), SPECC1L (Affinity Capture-MS), IGHA1 (Affinity Capture-MS), MNAT1 (Affinity Capture-MS), PIGR (Affinity Capture-MS), CA6 (Affinity Capture-MS), AMY1C (Affinity Capture-MS), CST1 (Affinity Capture-MS), CST4 (Affinity Capture-MS)

ESM2 similar proteins: A0A061AE05, A7SG48, B6LS00, C6BZQ4, D7EBK7, O17607, O45405, O59640, O94313, P05990, P06623, P07756, P09543, P0C920, P0C921, P0CN04, P0CN05, P0CR26, P0CR27, P19956, P20083, P27653, P31327, Q03940, Q08BN1, Q08BZ4, Q0VCR7, Q12663, Q3KNL4, Q3V3R1, Q44276, Q44277, Q5RFD0, Q5YLB4, Q6CFD2, Q6D421, Q7FAY6, Q7S8A6, Q8C196, Q8N6V4

Diamond homologs: A7SG48, B6LS00, P0C920, P0C921, Q08BN1, Q3KNL4, Q8N6V4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	4
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

404 predictions. Top by Δscore:

Variant	Effect	Δscore
10:49693768:TCCCA:T	acceptor_gain	1.0000
10:49693769:CCCA:C	acceptor_gain	1.0000
10:49693770:CCAGC:C	acceptor_gain	1.0000
10:49693771:CAGC:C	acceptor_gain	1.0000
10:49693772:A:AG	acceptor_gain	1.0000
10:49693772:AGCT:A	acceptor_gain	1.0000
10:49693772:AGCTG:A	acceptor_gain	1.0000
10:49693773:G:GC	acceptor_gain	1.0000
10:49693773:G:T	acceptor_gain	1.0000
10:49693773:GC:G	acceptor_gain	1.0000
10:49693773:GCT:G	acceptor_gain	1.0000
10:49693773:GCTG:G	acceptor_gain	1.0000
10:49693773:GCTGT:G	acceptor_gain	1.0000
10:49693775:T:A	acceptor_gain	1.0000
10:49693889:GTTCG:G	donor_gain	1.0000
10:49693894:G:GG	donor_gain	1.0000
10:49679791:CAAG:C	donor_loss	0.9900
10:49679792:AAG:A	donor_loss	0.9900
10:49679793:AGGTG:A	donor_loss	0.9900
10:49679794:GG:G	donor_loss	0.9900
10:49679795:G:A	donor_loss	0.9900
10:49679796:T:A	donor_loss	0.9900
10:49693890:TTCGG:T	donor_loss	0.9900
10:49693891:TCGG:T	donor_loss	0.9900
10:49693892:CG:C	donor_loss	0.9900
10:49693893:GGTAA:G	donor_loss	0.9900
10:49693894:GTAA:G	donor_loss	0.9900
10:49693895:T:G	donor_loss	0.9900
10:49693896:A:AG	donor_loss	0.9900
10:49679759:TG:T	donor_gain	0.9800

AlphaMissense

608 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
10:49693890:T:C	F72L	0.977
10:49693892:C:A	F72L	0.977
10:49693892:C:G	F72L	0.977
10:49693840:T:C	L55P	0.949
10:49679732:G:A	G12E	0.944
10:49694573:G:C	A85P	0.938
10:49679717:T:A	V7D	0.934
10:49693840:T:A	L55H	0.934
10:49693863:T:C	F63L	0.933
10:49693865:C:A	F63L	0.933
10:49693865:C:G	F63L	0.933
10:49693885:T:C	L70S	0.931
10:49694547:G:A	G76D	0.930
10:49694566:T:G	C82W	0.930
10:49694547:G:T	G76V	0.928
10:49679785:G:C	G30R	0.927
10:49693780:T:C	L35S	0.927
10:49679776:C:A	R27S	0.926
10:49679731:G:T	G12W	0.925
10:49694574:C:A	A85D	0.924
10:49679731:G:A	G12R	0.916
10:49679731:G:C	G12R	0.916
10:49694557:C:A	D79E	0.914
10:49694557:C:G	D79E	0.914
10:49694586:T:A	V89E	0.914
10:49694565:G:A	C82Y	0.907
10:49679780:T:C	L28P	0.904
10:49679726:G:C	R10P	0.897
10:49693840:T:G	L55R	0.896
10:49694582:G:C	A88P	0.896

dbSNP variants (sampled 300 via entrez): RS1000027292 (10:49698361 C>G), RS1000074469 (10:49698085 G>A,T), RS1000325547 (10:49709849 T>C), RS1000404546 (10:49685327 G>A), RS1000433445 (10:49697059 G>A), RS1000463700 (10:49684946 C>G,T), RS1000529102 (10:49692692 G>A,T), RS1000587111 (10:49703555 C>A), RS1000667517 (10:49682252 C>T), RS1000718933 (10:49688101 G>A,C,T), RS1000751862 (10:49688357 A>G), RS1000925449 (10:49679810 G>A,C,T), RS1001017042 (10:49682438 G>A), RS1001034060 (10:49699486 C>T), RS1001085849 (10:49699342 T>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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

5 total (human), top 5 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Arsenic	affects methylation	1
Benzo(a)pyrene	affects methylation, increases methylation	1
Malathion	decreases expression	1
Testosterone	decreases expression	1
Permethrin	decreases expression	1

Clinical trials (associated diseases)

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