PUS7L

Summary

PUS7L (pseudouridine synthase 7 like, HGNC:25276) is a protein-coding gene on chromosome 12q12, encoding Pseudouridylate synthase PUS7L (Q9H0K6). Pseudouridine synthase that catalyzes pseudouridylation of mRNAs.

Enables pseudouridine synthase activity. Involved in mRNA pseudouridine synthesis. Predicted to be active in nucleus.

Source: NCBI Gene 83448 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 98 total
• MANE Select transcript: NM_031292

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25276
Approved symbol	PUS7L
Name	pseudouridine synthase 7 like
Location	12q12
Locus type	gene with protein product
Status	Approved
Aliases	DKFZP434G1415
Ensembl gene	ENSG00000129317
Ensembl biotype	protein_coding
Entrez	83448

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 11 protein_coding, 1 non_stop_decay

ENST00000344862, ENST00000416848, ENST00000431332, ENST00000547156, ENST00000549868, ENST00000550784, ENST00000551923, ENST00000553166, ENST00000888397, ENST00000888398, ENST00000937009, ENST00000937010

RefSeq mRNA: 4 — MANE Select: NM_031292 NM_001098614, NM_001098615, NM_001271826, NM_031292

CCDS: CCDS61104, CCDS8743

Canonical transcript exons

ENST00000344862 — 9 exons

Exon	Start	End
ENSE00000887935	43731705	43731758
ENSE00000887936	43736381	43736661
ENSE00000887937	43738310	43738391
ENSE00000887938	43742457	43742555
ENSE00000887939	43746046	43746238
ENSE00001387849	43754336	43755261
ENSE00002345647	43718992	43730702
ENSE00002348564	43758730	43758790
ENSE00003637569	43748450	43748609

Expression profiles

Bgee: expression breadth ubiquitous, 251 present calls, max score 92.78.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 11.0293 / max 244.0114, expressed in 1678 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
130504	10.9170	1674
130503	0.1123	37

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
calcaneal tendon	UBERON:0003701	92.78	gold quality
colonic epithelium	UBERON:0000397	86.21	gold quality
secondary oocyte	CL:0000655	85.34	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.53	gold quality
olfactory bulb	UBERON:0002264	82.52	gold quality
adrenal tissue	UBERON:0018303	82.14	gold quality
tibia	UBERON:0000979	81.31	gold quality
cortical plate	UBERON:0005343	80.80	gold quality
corpus epididymis	UBERON:0004359	80.53	gold quality
corpus callosum	UBERON:0002336	80.44	gold quality
type B pancreatic cell	CL:0000169	80.32	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	80.04	gold quality
tonsil	UBERON:0002372	80.01	gold quality
bone marrow cell	CL:0002092	78.98	gold quality
islet of Langerhans	UBERON:0000006	78.92	gold quality
esophagus squamous epithelium	UBERON:0006920	78.91	gold quality
tendon	UBERON:0000043	78.86	gold quality
cauda epididymis	UBERON:0004360	77.84	gold quality
ganglionic eminence	UBERON:0004023	77.43	gold quality
stromal cell of endometrium	CL:0002255	76.99	gold quality
bone marrow	UBERON:0002371	76.94	gold quality
tongue squamous epithelium	UBERON:0006919	76.76	gold quality
ventricular zone	UBERON:0003053	76.70	gold quality
monocyte	CL:0000576	76.32	gold quality
Brodmann (1909) area 23	UBERON:0013554	76.17	gold quality
endothelial cell	CL:0000115	76.12	silver quality
mononuclear cell	CL:0000842	76.08	gold quality
caput epididymis	UBERON:0004358	76.03	gold quality
leukocyte	CL:0000738	75.93	gold quality
parietal pleura	UBERON:0002400	75.45	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	7.77
E-GEOD-110499	no	763.30

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

81 targeting PUS7L, 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-3163	100.00	77.23	8605
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-4500	99.99	72.72	2367
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-23A-3P	99.95	74.24	3163
HSA-MIR-23B-3P	99.95	74.24	3163
HSA-MIR-23C	99.95	73.92	3192
HSA-MIR-1236-3P	99.94	68.04	1695
HSA-MIR-8063	99.91	69.76	3146
HSA-MIR-10523-5P	99.91	69.22	2038
HSA-MIR-10527-5P	99.91	72.28	3754
HSA-MIR-3140-3P	99.88	68.47	2069
HSA-MIR-4760-5P	99.80	69.88	1619
HSA-MIR-4517	99.76	69.19	1867
HSA-MIR-623	99.76	68.16	1170
HSA-MIR-3617-5P	99.75	69.41	1968
HSA-MIR-641	99.75	69.35	1975
HSA-MIR-1255A	99.74	68.09	744
HSA-MIR-1255B-5P	99.74	68.16	741
HSA-MIR-4719	99.73	72.10	3329
HSA-MIR-4255	99.72	67.70	1541
HSA-MIR-4755-5P	99.71	70.34	2716
HSA-MIR-5006-3P	99.71	70.26	2728
HSA-MIR-494-3P	99.70	71.45	2795
HSA-MIR-5580-3P	99.70	69.41	2052

Literature-anchored findings (GeneRIF, showing 1)

• We have validated the vectors and confirmed self-association of AHCY, AHCYL1, and galectin-3. In a high-throughput BiFC screen, we identified new AHCY interaction partners: galectin-3 and PUS7L. We also describe additional steps in protein interaction analysis, applied for AHCY-galectin-3 interaction (PMID:27455993)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	pus7l	ENSDARG00000069780
mus_musculus	Pus7l	ENSMUSG00000033356
rattus_norvegicus	Pus7l	ENSRNOG00000022570
caenorhabditis_elegans		WBGENE00007101

Paralogs (1): PUS7 (ENSG00000091127)

Protein

Protein identifiers

Pseudouridylate synthase PUS7L — Q9H0K6 (reviewed: Q9H0K6)

Alternative names: Pseudouridylate synthase 7 homolog-like protein

All UniProt accessions (5): Q9H0K6, F8VP66, F8VW99, F8VWC0, F8VZA0

UniProt curated annotations — full annotation on UniProt →

Function. Pseudouridine synthase that catalyzes pseudouridylation of mRNAs.

Similarity. Belongs to the pseudouridine synthase TruD family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9H0K6-1	1	yes
Q9H0K6-2	2

RefSeq proteins (4): NP_001092084, NP_001092085, NP_001258755, NP_112582* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001656	PsdUridine_synth_TruD	Family
IPR011760	PsdUridine_synth_TruD_insert	Domain
IPR020103	PsdUridine_synth_cat_dom_sf	Homologous_superfamily
IPR042214	TruD_catalytic	Homologous_superfamily
IPR056961	R3H_PUS7L	Domain
IPR056963	PUS7L_N	Domain

Pfam: PF01142, PF23943, PF25094

Catalyzed reactions (Rhea), 1 shown:

• a uridine in mRNA = a pseudouridine in mRNA (RHEA:56644)

UniProt features (11 total): sequence conflict 3, sequence variant 3, chain 1, domain 1, active site 1, modified residue 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9H0K6-F1	76.90	0.38

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (1): 339 (nucleophile)

Post-translational modifications (1): 79

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 98 (showing top): TGCGCANK_UNKNOWN, chr12q12, IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR, GOBP_MRNA_MODIFICATION, GOBP_PSEUDOURIDINE_SYNTHESIS, GOBP_RNA_MODIFICATION, KOYAMA_SEMA3B_TARGETS_UP, PU1_Q6, DODD_NASOPHARYNGEAL_CARCINOMA_UP, RYTTCCTG_ETS2_B, ZHANG_BREAST_CANCER_PROGENITORS_UP, RGAGGAARY_PU1_Q6, CTGYNNCTYTAA_UNKNOWN, ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, GOMF_PSEUDOURIDINE_SYNTHASE_ACTIVITY

GO Biological Process (5): pseudouridine synthesis (GO:0001522), mRNA processing (GO:0006397), mRNA pseudouridine synthesis (GO:1990481), tRNA processing (GO:0008033), RNA modification (GO:0009451)

GO Molecular Function (4): RNA binding (GO:0003723), pseudouridine synthase activity (GO:0009982), protein binding (GO:0005515), isomerase activity (GO:0016853)

GO Cellular Component (1): nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
RNA processing	2
RNA modification	1
mRNA metabolic process	1
pseudouridine synthesis	1
mRNA modification	1
tRNA metabolic process	1
RNA metabolic process	1
macromolecule modification	1
nucleic acid binding	1
intramolecular transferase activity	1
binding	1
catalytic activity	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

1575 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PUS7L	TRUB2	O95900	810
PUS7L	PUS10	Q3MIT2	793
PUS7L	RPUSD1	Q9UJJ7	793
PUS7L	TRUB1	Q8WWH5	781
PUS7L	RPUSD2	Q8IZ73	776
PUS7L	PUS3	Q9BZE2	773
PUS7L	PUS1	Q9Y606	771
PUS7L	RPUSD3	Q6P087	763
PUS7L	RPUSD4	Q96CM3	744
PUS7L	PUSL1	Q8N0Z8	709
PUS7L	DKC1	O60832	557
PUS7L	NOP10	Q9NPE3	528
PUS7L	ZFYVE19	Q96K21	504
PUS7L	NHP2	Q9NX24	494
PUS7L	CCDC88B	A6NC98	439

IntAct

18 interactions, top by confidence:

A	B	Type	Score
PUS7L	TRIM27	psi-mi:“MI:0915”(physical association)	0.780
TRIM27	PUS7L	psi-mi:“MI:0915”(physical association)	0.780
PUS7L	TRIM41	psi-mi:“MI:0915”(physical association)	0.560
TRIM41	PUS7L	psi-mi:“MI:0915”(physical association)	0.560
ARIH1	SPOP	psi-mi:“MI:0914”(association)	0.530
STAT5B	PDHX	psi-mi:“MI:0914”(association)	0.350
GAK	PARP10	psi-mi:“MI:0914”(association)	0.350
PTGES3	SBNO1	psi-mi:“MI:0914”(association)	0.350
	SUPT5H	psi-mi:“MI:0914”(association)	0.350
ARIH1	PHGDH	psi-mi:“MI:0914”(association)	0.350
PUS7L	PRPS2	psi-mi:“MI:0914”(association)	0.350
PUS7L	TRIM27	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (23): PUS7L (Two-hybrid), TRIM41 (Two-hybrid), PUS7L (Affinity Capture-MS), PUS7L (Affinity Capture-MS), PUS7L (Affinity Capture-MS), PUS7L (Affinity Capture-MS), TRIM27 (Two-hybrid), PUS7L (Affinity Capture-MS), EPS8L2 (Affinity Capture-MS), PUS7L (Affinity Capture-MS), PRPS2 (Affinity Capture-MS), PUS7L (Affinity Capture-MS), PUS7L (Co-fractionation), PUS7L (Proximity Label-MS), PUS7L (Proximity Label-MS)

ESM2 similar proteins: A2VE39, A7YT82, D2HRF1, F6VSS6, O14730, O60551, O70310, P30419, P31717, P49916, P97386, Q08DI8, Q1L8I0, Q1RMT7, Q28E61, Q2T9V5, Q2VPA6, Q32P41, Q3MIT2, Q4KLT3, Q4V7N2, Q5R981, Q5RAF3, Q5U2Z5, Q5ZLV4, Q6GQ76, Q6ING2, Q6NS23, Q7SXA9, Q803R5, Q8BYH3, Q8CE46, Q8CE96, Q8K1Q0, Q8K4M9, Q8N1G2, Q91VU7, Q91XL9, Q96PZ0, Q9BXW6

Diamond homologs: A1TZ52, A1W165, A4FYL2, A4VJV1, A5ICB9, A5UE25, A5W822, A6Q2U7, A6UV17, A7H5G6, A7HGV2, A8FNC4, B0KSC6, B0RU01, B0URU7, B1JB31, B2UU74, B3PJA9, B5Z7T0, B6JME7, B6YTE4, B7V8C2, B8J7C8, B9M644, C1DSR9, C3K704, C6A1K9, O27572, O28596, O74343, P44039, P55985, P59892, P59893, Q08647, Q08DI8, Q0I5H8, Q12WH6, Q17426, Q17WX3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	84
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1862 predictions. Top by Δscore:

Variant	Effect	Δscore
12:43730596:TTAA:T	donor_gain	1.0000
12:43730605:CATGT:C	donor_gain	1.0000
12:43731161:G:C	donor_gain	1.0000
12:43746040:TCTTA:T	donor_loss	1.0000
12:43746041:CTTA:C	donor_loss	1.0000
12:43746042:TTAC:T	donor_loss	1.0000
12:43746043:TACCT:T	donor_loss	1.0000
12:43746044:ACCTT:A	donor_loss	1.0000
12:43746045:C:CG	donor_loss	1.0000
12:43746234:TCAAC:T	acceptor_gain	1.0000
12:43746235:CAAC:C	acceptor_gain	1.0000
12:43746235:CAACC:C	acceptor_gain	1.0000
12:43746238:CCTGT:C	acceptor_loss	1.0000
12:43746239:C:CA	acceptor_loss	1.0000
12:43746239:C:CC	acceptor_gain	1.0000
12:43746240:T:C	acceptor_loss	1.0000
12:43748444:TATTA:T	donor_loss	1.0000
12:43748446:TTA:T	donor_loss	1.0000
12:43748447:TA:T	donor_loss	1.0000
12:43748449:CCT:C	donor_gain	1.0000
12:43748449:CCTCT:C	donor_gain	1.0000
12:43748605:AAAAG:A	acceptor_gain	1.0000
12:43748606:AAAG:A	acceptor_gain	1.0000
12:43748607:AAG:A	acceptor_gain	1.0000
12:43748608:AG:A	acceptor_gain	1.0000
12:43748610:C:A	acceptor_loss	1.0000
12:43748610:C:CC	acceptor_gain	1.0000
12:43748611:T:G	acceptor_loss	1.0000
12:43755261:CCTA:C	acceptor_loss	1.0000
12:43755262:C:CC	acceptor_gain	1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000160876 (12:43744479 G>A,T), RS1000200996 (12:43742935 T>C), RS1000219712 (12:43733982 G>A,C), RS1000270412 (12:43733611 G>C,T), RS1000307310 (12:43753101 C>T), RS1000402656 (12:43730979 A>G), RS1000429515 (12:43740059 T>G), RS1000606363 (12:43735151 T>G), RS1000669002 (12:43737593 T>C,G), RS1000817919 (12:43741498 C>T), RS1000885205 (12:43731304 GA>G), RS1000885259 (12:43739653 G>A), RS1000891984 (12:43720276 G>A), RS1001054844 (12:43727791 T>C), RS1001087647 (12:43718649 C>T)

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
GCST001536_6	Immune reponse to smallpox (secreted TNF-alpha)	2.000000e-08
GCST003602_9	Inflammatory bowel disease	6.000000e-06
GCST009391_499	Metabolite levels	1.000000e-06

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0004645	response to vaccine
EFO:0004873	cytokine measurement
EFO:0010521	phosphocreatine measurement

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
Estradiol	increases expression	2
Cyclosporine	increases expression	2
Cadmium Chloride	increases abundance, increases expression, decreases expression	2
dicrotophos	decreases expression	1
alpha phellandrene	decreases expression	1
triphenyl phosphate	affects expression	1
kojic acid	decreases expression	1
sodium arsenite	decreases expression	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
coumarin	decreases phosphorylation	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
perfluorooctane sulfonic acid	decreases expression	1
ICG 001	increases expression	1
abrine	decreases expression	1
jinfukang	decreases expression	1
Sunitinib	decreases expression	1
Vorinostat	increases expression	1
Atrazine	decreases expression	1
Cadmium	increases abundance, increases expression	1
Dimethyl Sulfoxide	increases expression	1
Doxorubicin	decreases expression	1
Ethyl Methanesulfonate	decreases expression	1
Formaldehyde	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Tretinoin	decreases expression	1
Urethane	decreases expression	1
Valproic Acid	decreases methylation	1
Aflatoxin B1	decreases methylation	1
Aflatoxin M1	decreases expression	1
Copper Sulfate	decreases expression	1

Clinical trials (associated diseases)

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