UTP14A

Summary

UTP14A (UTP14A small subunit processome component, HGNC:10665) is a protein-coding gene on chromosome Xq26.1, encoding U3 small nucleolar RNA-associated protein 14 homolog A (Q9BVJ6). May be required for ribosome biogenesis.

This gene encodes a member of the uridine triphosphate 14 family. As an essential component of a large ribonucleoprotein complex bound to the U3 small nucleolar RNA, the encoded protein is involved in ribosome biogenesis and 18S rRNA synthesis. An autosomal retrotransposed copy of this X-linked gene exists on chromosome 13. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 10813 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 8 total
• MANE Select transcript: NM_006649

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:10665
Approved symbol	UTP14A
Name	UTP14A small subunit processome component
Location	Xq26.1
Locus type	gene with protein product
Status	Approved
Aliases	NY-CO-16, Utp14
Ensembl gene	ENSG00000156697
Ensembl biotype	protein_coding
OMIM	300508
Entrez	10813

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 7 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000394422, ENST00000425117, ENST00000427972, ENST00000498179, ENST00000869131, ENST00000869132, ENST00000956765, ENST00000956766

RefSeq mRNA: 2 — MANE Select: NM_006649 NM_001166221, NM_006649

CCDS: CCDS14615, CCDS55489

Canonical transcript exons

ENST00000394422 — 15 exons

Exon	Start	End
ENSE00000676407	129908670	129908734
ENSE00000676408	129911008	129911150
ENSE00001027863	129925919	129926112
ENSE00001027864	129921194	129921587
ENSE00001027866	129920675	129920752
ENSE00001027867	129919395	129919489
ENSE00001027870	129920457	129920580
ENSE00001027872	129924795	129925195
ENSE00001027874	129929336	129929752
ENSE00001027878	129926240	129926339
ENSE00001144953	129911766	129911921
ENSE00001165997	129919175	129919294
ENSE00001628354	129906164	129906236
ENSE00003490078	129907367	129907442
ENSE00003668627	129908060	129908130

Expression profiles

Bgee: expression breadth ubiquitous, 265 present calls, max score 98.34.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 21.3796 / max 391.7811, expressed in 1802 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
197538	19.4102	1802
197537	1.9694	1140

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
oocyte	CL:0000023	98.34	gold quality
secondary oocyte	CL:0000655	94.67	gold quality
gingival epithelium	UBERON:0001949	91.10	gold quality
gingiva	UBERON:0001828	90.19	gold quality
squamous epithelium	UBERON:0006914	89.47	gold quality
esophagus squamous epithelium	UBERON:0006920	89.01	gold quality
cervix squamous epithelium	UBERON:0006922	88.93	silver quality
parotid gland	UBERON:0001831	88.59	gold quality
parietal pleura	UBERON:0002400	88.31	gold quality
middle temporal gyrus	UBERON:0002771	87.86	gold quality
germinal epithelium of ovary	UBERON:0001304	87.62	gold quality
amniotic fluid	UBERON:0000173	87.35	gold quality
colonic epithelium	UBERON:0000397	87.10	gold quality
pleura	UBERON:0000977	86.66	gold quality
epithelium of esophagus	UBERON:0001976	86.49	gold quality
tibia	UBERON:0000979	86.10	gold quality
visceral pleura	UBERON:0002401	85.44	gold quality
Brodmann (1909) area 23	UBERON:0013554	85.44	gold quality
oral cavity	UBERON:0000167	85.41	gold quality
body of pancreas	UBERON:0001150	85.11	gold quality
monocyte	CL:0000576	84.87	gold quality
pancreas	UBERON:0001264	84.69	gold quality
mononuclear cell	CL:0000842	84.68	gold quality
mucosa of sigmoid colon	UBERON:0004993	84.59	gold quality
leukocyte	CL:0000738	84.58	gold quality
tonsil	UBERON:0002372	84.55	gold quality
palpebral conjunctiva	UBERON:0001812	84.31	gold quality
islet of Langerhans	UBERON:0000006	84.14	gold quality
trabecular bone tissue	UBERON:0002483	83.80	gold quality
colonic mucosa	UBERON:0000317	83.37	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.29
E-GEOD-99795	no	98.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

9 targeting UTP14A, 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-3121-3P	99.82	71.96	3630
HSA-MIR-10A-5P	98.89	69.85	712
HSA-MIR-10B-5P	98.89	69.86	711
HSA-MIR-1199-5P	98.44	66.51	829
HSA-MIR-6751-3P	98.44	66.35	835
HSA-MIR-532-5P	98.43	67.53	760
HSA-MIR-4776-5P	97.14	66.63	405
HSA-MIR-4474-3P	96.97	65.87	870
HSA-MIR-3654	96.43	66.55	646

Literature-anchored findings (GeneRIF, showing 7)

• hUTP14a physically interacts with p53 and functionally promotes p53 turn-over (PMID:21078665)
• The positivity rate of hUTP14a expression was significantly higher in HCC specimens. Positive expression of nucleolar hUTP14a might act as a novel prognostic predictor for patients with HCC (PMID:28218222)
• The hUTP14a protected tumor cells from chemotherapeutic drug-induced apoptosis and thus might possess a potential as a target for anti-tumor therapy. (PMID:28672776)
• hUTP14a interacts with c-Myc and protects c-Myc from ubiquitination and degradation in a USP36-dependent way. (PMID:30343112)
• suggesting that hUTP14a might possess a potential as a candidate marker for the early diagnosis screening of non-small cell lung cancer (PMID:30773559)
• UTP14a promotes angiogenesis through upregulating transcription and secretion of PDGFA in colorectal cancer. (PMID:30929921)
• Results suggest that UTP14a expression is correlated with tumor proliferation and invasion; higher expression of UTP14a is a predictor of poor prognosis in patients with esophageal squamous cell carcinoma (ESCC). Additionally, knockdown of UTP14a inhibits cell proliferation and invasion in ESCC cell line, ECA109. (PMID:31496055)

Cross-species orthologs

7 orthologs

Organism	Symbol	Gene ID
danio_rerio	UTP14A	ENSDARG00000042520
mus_musculus	Utp14a	ENSMUSG00000063785
mus_musculus	Utp14b	ENSMUSG00000079470
rattus_norvegicus	Utp14a	ENSRNOG00000005012
rattus_norvegicus	LOC102551819	ENSRNOG00000063437
drosophila_melanogaster	CG12301	FBGN0036514
caenorhabditis_elegans	F27C1.6	WBGENE00017855

Paralogs (1): UTP14C (ENSG00000253797)

Protein

Protein identifiers

U3 small nucleolar RNA-associated protein 14 homolog A — Q9BVJ6 (reviewed: Q9BVJ6)

Alternative names: Antigen NY-CO-16, Serologically defined colon cancer antigen 16

All UniProt accessions (2): Q9BVJ6, X6RJY0

UniProt curated annotations — full annotation on UniProt →

Function. May be required for ribosome biogenesis.

Subunit / interactions. Interacts with DHX37.

Subcellular location. Nucleus. Nucleolus.

Tissue specificity. Ubiquitously expressed.

Post-translational modifications. Citrullinated by PADI4.

Miscellaneous. The human genome also contains the UTP14C gene, an autosomal retrotransposed copy of this X-linked gene. Evolution of autosomal retrogenes from X-linked progenitors compensates for X-chromosome silencing during male meiosis.

Similarity. Belongs to the UTP14 family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q9BVJ6-1	1	yes
Q9BVJ6-2	2
Q9BVJ6-3	3

RefSeq proteins (2): NP_001159693, NP_006640* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR006709	SSU_processome_Utp14	Family

Pfam: PF04615

UniProt features (42 total): modified residue 14, compositionally biased region 7, region of interest 4, cross-link 4, splice variant 3, sequence variant 3, coiled-coil region 3, helix 2, chain 1, strand 1

Structure

Experimental structures (PDB)

4 structures.

PDB	Method	Resolution (Å)
7MQA	ELECTRON MICROSCOPY	2.7
7WTS	ELECTRON MICROSCOPY	3.2
7MQ8	ELECTRON MICROSCOPY	3.6
7MQ9	ELECTRON MICROSCOPY	3.87

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BVJ6-F1	66.74	0.21

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 (18): 29, 31, 52, 77, 81, 205, 405, 407, 433, 437, 445, 453, 569, 589, 122, 449, 519, 733

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

ID	Pathway
R-HSA-6790901	rRNA modification in the nucleus and cytosol
R-HSA-6791226	Major pathway of rRNA processing in the nucleolus and cytosol

MSigDB gene sets: 125 (showing top): GOBP_RIBOSOME_BIOGENESIS, GOBP_MATURATION_OF_SSU_RRNA, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_1, MILI_PSEUDOPODIA_HAPTOTAXIS_UP, CHIARADONNA_NEOPLASTIC_TRANSFORMATION_CDC25_UP, GOBP_RIBOSOMAL_SMALL_SUBUNIT_BIOGENESIS, AGGAGTG_MIR483, DODD_NASOPHARYNGEAL_CARCINOMA_UP, USF_02, GOBP_RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS, REACTOME_METABOLISM_OF_RNA, TGGAAA_NFAT_Q4_01, GOCC_PRERIBOSOME, GOCC_SMALL_SUBUNIT_PROCESSOME, GOCC_NUCLEOLUS

GO Biological Process (2): rRNA processing (GO:0006364), ribosome biogenesis (GO:0042254)

GO Molecular Function (2): RNA binding (GO:0003723), protein binding (GO:0005515)

GO Cellular Component (5): nucleoplasm (GO:0005654), nucleolus (GO:0005730), cytosol (GO:0005829), small-subunit processome (GO:0032040), nucleus (GO:0005634)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
rRNA processing in the nucleus and cytosol	2

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
nuclear lumen	2
cellular anatomical structure	2
RNA processing	1
rRNA metabolic process	1
ribosome biogenesis	1
ribonucleoprotein complex biogenesis	1
nucleic acid binding	1
binding	1
intracellular membraneless organelle	1
cytoplasm	1
nucleolus	1
preribosome	1
t-UTP complex	1
nuclear protein-containing complex	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

2377 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
UTP14A	WDR46	O15213	920
UTP14A	UTP6	Q9NYH9	843
UTP14A	NOP14	P78316	811
UTP14A	UTP3	Q9NQZ2	785
UTP14A	RCL1	Q9Y2P8	772
UTP14A	PWP2	Q15269	768
UTP14A	UTP20	O75691	756
UTP14A	BMS1	Q14692	756
UTP14A	NAT10	Q9H0A0	752
UTP14A	DHX37	Q8IY37	743
UTP14A	FCF1	Q9Y324	722
UTP14A	PNO1	Q9NRX1	704
UTP14A	UTP15	Q8TED0	704
UTP14A	USP36	Q9P275	702
UTP14A	PDCD11	Q14690	698

IntAct

193 interactions, top by confidence:

A	B	Type	Score
PES1	BOP1	psi-mi:“MI:0914”(association)	0.810
CFTR	ESYT2	psi-mi:“MI:2364”(proximity)	0.710
SMYD1	UTP14A	psi-mi:“MI:0915”(physical association)	0.670
HTT	UTP14A	psi-mi:“MI:0915”(physical association)	0.670
UTP14A	SMYD1	psi-mi:“MI:0915”(physical association)	0.670
ESR1	TRIM24	psi-mi:“MI:0914”(association)	0.640
GADD45G	UTP14A	psi-mi:“MI:0915”(physical association)	0.630
UTP14A	GADD45G	psi-mi:“MI:0915”(physical association)	0.630
NPM1	MPHOSPH10	psi-mi:“MI:0914”(association)	0.610
LMO1	UTP14A	psi-mi:“MI:0915”(physical association)	0.560
TXLNB	UTP14A	psi-mi:“MI:0915”(physical association)	0.560
UTP14A	A2M	psi-mi:“MI:0915”(physical association)	0.560
UTP14A	APLP2	psi-mi:“MI:0915”(physical association)	0.560
UTP14A	BLMH	psi-mi:“MI:0915”(physical association)	0.560
UTP14A	CAMK2A	psi-mi:“MI:0915”(physical association)	0.560
UTP14A	CSNK1D	psi-mi:“MI:0915”(physical association)	0.560
DYNC1I1	UTP14A	psi-mi:“MI:0915”(physical association)	0.560
RAC1	UTP14A	psi-mi:“MI:0915”(physical association)	0.560
UTP14A	ATXN10	psi-mi:“MI:0915”(physical association)	0.560
UTP14A	JPH3	psi-mi:“MI:0915”(physical association)	0.560
APP	UTP14A	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (291): UTP14A (Affinity Capture-MS), UTP14A (Affinity Capture-MS), UTP14A (Affinity Capture-MS), UTP14A (Affinity Capture-MS), NINL (Two-hybrid), CEP70 (Two-hybrid), LDOC1 (Two-hybrid), CCDC85B (Two-hybrid), HOOK2 (Two-hybrid), UTP14A (Affinity Capture-MS), DKC1 (Co-fractionation), NOP56 (Co-fractionation), NOP58 (Co-fractionation), RPF2 (Co-fractionation), UTP14A (Co-fractionation)

ESM2 similar proteins: A1A5P2, A6QNR1, A8WY26, D3ZND0, O15213, O59678, P27672, P78316, Q0V8M0, Q15050, Q24K12, Q28IV8, Q2KIH4, Q2KII6, Q3T0Q8, Q3T0Z5, Q3UFY0, Q4KLC4, Q5M985, Q5RAS1, Q5RJT2, Q5TAP6, Q5TJE7, Q5ZKM1, Q640M1, Q6EJB6, Q6P0I6, Q6PFJ1, Q8BK35, Q8IY81, Q8N9T8, Q8NEJ9, Q8R3N1, Q8VDQ9, Q96BZ8, Q96EU6, Q9BRP8, Q9BRR8, Q9BVJ6, Q9C086

Diamond homologs: Q3T0Q8, Q5TAP6, Q640M1, Q6EJB6, Q9BVJ6

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 183 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
SARS-CoV-1 modulates host translation machinery	6	14.6×	3e-04
rRNA processing in the nucleus and cytosol	10	12.7×	1e-06
Eukaryotic Translation Initiation	5	12.2×	2e-03
Cap-dependent Translation Initiation	5	12.2×	2e-03
rRNA processing	10	11.5×	2e-06
Eukaryotic Translation Elongation	5	11.0×	2e-03
Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S	5	10.7×	2e-03
Major pathway of rRNA processing in the nucleolus and cytosol	21	10.2×	7e-13

GO biological processes:

GO term	Partners	Fold	FDR
maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	6	24.1×	5e-05
ribosomal small subunit biogenesis	8	10.8×	2e-04
cytoplasmic translation	8	8.8×	5e-04
RNA splicing	15	7.9×	9e-07
mRNA splicing, via spliceosome	14	7.6×	3e-06
rRNA processing	9	7.6×	5e-04
mRNA processing	13	6.1×	7e-05

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	2
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1810 predictions. Top by Δscore:

Variant	Effect	Δscore
X:129907362:A:AG	acceptor_gain	1.0000
X:129907363:A:G	acceptor_gain	1.0000
X:129907363:ACAG:A	acceptor_loss	1.0000
X:129907364:CA:C	acceptor_loss	1.0000
X:129907365:A:AG	acceptor_gain	1.0000
X:129907365:A:C	acceptor_loss	1.0000
X:129907366:G:GG	acceptor_gain	1.0000
X:129907366:GC:G	acceptor_gain	1.0000
X:129907366:GCC:G	acceptor_gain	1.0000
X:129907366:GCCT:G	acceptor_gain	1.0000
X:129907366:GCCTT:G	acceptor_gain	1.0000
X:129907442:GGTG:G	donor_loss	1.0000
X:129907443:GTG:G	donor_loss	1.0000
X:129907444:T:G	donor_loss	1.0000
X:129908099:G:GT	donor_gain	1.0000
X:129908122:A:T	donor_gain	1.0000
X:129908664:TTTCA:T	acceptor_loss	1.0000
X:129908665:TTCA:T	acceptor_loss	1.0000
X:129908666:TCA:T	acceptor_loss	1.0000
X:129908667:CAGG:C	acceptor_loss	1.0000
X:129908733:AGGTA:A	donor_loss	1.0000
X:129908734:GGT:G	donor_loss	1.0000
X:129911005:CAGG:C	acceptor_loss	1.0000
X:129911006:A:AG	acceptor_gain	1.0000
X:129911006:AG:A	acceptor_gain	1.0000
X:129911007:G:GG	acceptor_gain	1.0000
X:129911007:GG:G	acceptor_gain	1.0000
X:129911148:CGGG:C	donor_loss	1.0000
X:129911149:GG:G	donor_gain	1.0000
X:129911150:GG:G	donor_gain	1.0000

AlphaMissense

5063 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:129919452:G:C	A239P	0.996
X:129920693:C:G	H299D	0.994
X:129920713:G:C	W305C	0.994
X:129920713:G:T	W305C	0.994
X:129911814:T:A	W144R	0.993
X:129911814:T:C	W144R	0.993
X:129919440:T:C	S235P	0.993
X:129920680:A:C	R294S	0.993
X:129920680:A:T	R294S	0.993
X:129920695:C:A	H299Q	0.993
X:129920695:C:G	H299Q	0.993
X:129926060:T:A	W631R	0.993
X:129926060:T:C	W631R	0.993
X:129926069:T:A	W634R	0.993
X:129926069:T:C	W634R	0.993
X:129919429:G:C	R231P	0.992
X:129919458:G:C	A241P	0.992
X:129926071:G:C	W634C	0.992
X:129926071:G:T	W634C	0.992
X:129919417:T:C	L227P	0.991
X:129920688:T:C	L297P	0.991
X:129920711:T:A	W305R	0.991
X:129920711:T:C	W305R	0.991
X:129926062:G:C	W631C	0.991
X:129926062:G:T	W631C	0.991
X:129911816:G:C	W144C	0.990
X:129911816:G:T	W144C	0.990
X:129919395:G:C	A220P	0.990
X:129919435:T:C	L233P	0.990
X:129919482:A:C	S249R	0.990

dbSNP variants (sampled 300 via entrez): RS1000148586 (X:129918684 C>T), RS1000200316 (X:129914143 C>T), RS1000252682 (X:129914525 C>T), RS1000357700 (X:129924016 G>A), RS1000537632 (X:129912398 G>A,C), RS1000765385 (X:129920959 A>C), RS1000829734 (X:129923555 G>A), RS1001056272 (X:129919039 C>G), RS1001094491 (X:129921531 G>A,T), RS1001229863 (X:129907719 G>A), RS1001257574 (X:129916072 G>C,T), RS1001258447 (X:129916366 C>T), RS1001641086 (X:129907179 T>C), RS1001755191 (X:129917574 C>T), RS1001946042 (X:129929841 G>A)

Disease associations

OMIM: gene MIM:300508 | 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

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	affects cotreatment, increases abundance, increases expression, decreases expression	2
Valproic Acid	affects expression, increases expression	2
Cyclosporine	increases expression	2
aristolochic acid I	decreases expression	1
TAK-243	affects sumoylation	1
dicrotophos	decreases expression	1
triphenyl phosphate	affects expression	1
deoxynivalenol	increases expression	1
sodium arsenate	decreases expression	1
manganese chloride	affects cotreatment, increases abundance, increases expression	1
potassium chromate(VI)	affects cotreatment, increases expression	1
coumarin	affects phosphorylation	1
beta-methylcholine	affects expression	1
epigallocatechin gallate	affects cotreatment, increases expression	1
di-n-butylphosphoric acid	affects expression	1
2,3,5-(triglutathion-S-yl)hydroquinone	increases ADP-ribosylation	1
deguelin	increases expression	1
abrine	increases expression	1
pyrachlostrobin	increases expression	1
jinfukang	affects cotreatment, decreases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	decreases expression	1
Sunitinib	decreases expression	1
Antimycin A	increases expression	1
Arsenic	affects cotreatment, increases abundance, increases expression	1
Benzo(a)pyrene	affects methylation, increases methylation	1
Caffeine	affects phosphorylation	1
Cisplatin	affects cotreatment, decreases expression	1
Curcumin	increases expression	1
Dichlorodiphenyl Dichloroethylene	increases expression	1
Diazinon	decreases methylation	1

Clinical trials (associated diseases)

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