TENT2

Summary

TENT2 (terminal nucleotidyltransferase 2, HGNC:26776) is a protein-coding gene on chromosome 5q14.1, encoding Poly(A) RNA polymerase GLD2 (Q6PIY7). Cytoplasmic poly(A) RNA polymerase that adds successive AMP monomers to the 3’-end of specific RNAs, forming a poly(A) tail.

Enables poly(A) RNA polymerase activity. Involved in histone mRNA catabolic process; mRNA 3’-end processing; and negative regulation of miRNA catabolic process. Predicted to be located in cytoplasm and nucleus. Predicted to be part of nuclear RNA-directed RNA polymerase complex. Predicted to be active in glutamatergic synapse; perforant pathway to dendrate granule cell synapse; and postsynapse.

Source: NCBI Gene 167153 — RefSeq curated summary.

At a glance

• GWAS associations: 15
• Clinical variants (ClinVar): 81 total — 1 pathogenic
• MANE Select transcript: NM_001114394

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26776
Approved symbol	TENT2
Name	terminal nucleotidyltransferase 2
Location	5q14.1
Locus type	gene with protein product
Status	Approved
Aliases	FLJ38499, GLD2, TUT2
Ensembl gene	ENSG00000164329
Ensembl biotype	protein_coding
OMIM	614121
Entrez	167153

Gene structure

Transcript identifiers

Ensembl transcripts: 55 — 43 protein_coding, 7 protein_coding_CDS_not_defined, 5 retained_intron

ENST00000296783, ENST00000423041, ENST00000453514, ENST00000502269, ENST00000503620, ENST00000504233, ENST00000504982, ENST00000505571, ENST00000505770, ENST00000508620, ENST00000509227, ENST00000510721, ENST00000513735, ENST00000514095, ENST00000515298, ENST00000515807, ENST00000885998, ENST00000885999, ENST00000886000, ENST00000886001, ENST00000886002, ENST00000886003, ENST00000886004, ENST00000886005, ENST00000886006, ENST00000886007, ENST00000886008, ENST00000886009, ENST00000886010, ENST00000886011, ENST00000886012, ENST00000886013, ENST00000886014, ENST00000886015, ENST00000886016, ENST00000886017, ENST00000886018, ENST00000886019, ENST00000886020, ENST00000923578, ENST00000923579, ENST00000923580, ENST00000947496, ENST00000947497, ENST00000947498, ENST00000947499, ENST00000947500, ENST00000947501, ENST00000947502, ENST00000947503, ENST00000947504, ENST00000947505, ENST00000947506, ENST00000947507, ENST00000947508

RefSeq mRNA: 56 — MANE Select: NM_001114394 NM_001114393, NM_001114394, NM_001297744, NM_001297745, NM_001349548, NM_001349549, NM_001349550, NM_001349551, NM_001349552, NM_001349553, NM_001349554, NM_001388093, NM_001388094, NM_001388095, NM_001388096, NM_001388097, NM_001388098, NM_001388099, NM_001388100, NM_001388101, NM_001388102, NM_001388103, NM_001388105, NM_001388106, NM_001388107, NM_001388108, NM_001388109, NM_001388110, NM_001388111, NM_001388112, NM_001388113, NM_001388114, NM_001388115, NM_001388116, NM_001388117, NM_001388118, NM_001388119, NM_001388120, NM_001388121, NM_001388122, NM_001388123, NM_001388124, NM_001388125, NM_001388126, NM_001388127, NM_001388128, NM_001388129, NM_001388130, NM_001388131, NM_001388132, NM_001388133, NM_001388134, NM_001388135, NM_001388136, NM_001388137, NM_173797

CCDS: CCDS4048, CCDS75265, CCDS75266

Canonical transcript exons

ENST00000453514 — 15 exons

Exon	Start	End
ENSE00001083575	79641105	79641196
ENSE00001083578	79642832	79642910
ENSE00001083579	79648617	79648693
ENSE00001083580	79649062	79649190
ENSE00001083581	79640851	79640965
ENSE00001083583	79623252	79623489
ENSE00001083584	79645123	79645192
ENSE00001603657	79612441	79613075
ENSE00003507733	79619994	79620083
ENSE00003517028	79656958	79657001
ENSE00003623004	79668892	79669028
ENSE00003628895	79619612	79619785
ENSE00003649086	79679579	79679670
ENSE00003691334	79681982	79682061
ENSE00003916469	79685199	79688246

Expression profiles

Bgee: expression breadth ubiquitous, 260 present calls, max score 97.49.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 46.7084 / max 379.9191, expressed in 1824 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter ID	TPM avg	Samples expressed
57243	31.6189	1821
57246	8.1842	1538
57244	2.7765	1271
57247	1.3857	721
57245	1.0700	573
57249	0.6541	369
57248	0.5227	289
57250	0.4963	130

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
calcaneal tendon	UBERON:0003701	97.49	gold quality
secondary oocyte	CL:0000655	97.31	gold quality
corpus epididymis	UBERON:0004359	97.05	gold quality
caput epididymis	UBERON:0004358	96.51	gold quality
cauda epididymis	UBERON:0004360	96.26	gold quality
colonic epithelium	UBERON:0000397	96.10	gold quality
adrenal tissue	UBERON:0018303	95.87	gold quality
oocyte	CL:0000023	95.66	gold quality
thymus	UBERON:0002370	95.16	gold quality
monocyte	CL:0000576	94.90	gold quality
corpus callosum	UBERON:0002336	94.87	gold quality
leukocyte	CL:0000738	94.80	gold quality
sural nerve	UBERON:0015488	94.72	gold quality
bone marrow	UBERON:0002371	94.57	gold quality
bone marrow cell	CL:0002092	94.55	gold quality
skin of abdomen	UBERON:0001416	94.42	gold quality
left ovary	UBERON:0002119	94.32	gold quality
tibial nerve	UBERON:0001323	94.20	gold quality
mucosa of stomach	UBERON:0001199	94.18	gold quality
spleen	UBERON:0002106	94.12	gold quality
trabecular bone tissue	UBERON:0002483	93.98	gold quality
skin of leg	UBERON:0001511	93.96	gold quality
right ovary	UBERON:0002118	93.96	gold quality
lymph node	UBERON:0000029	93.80	gold quality
right lung	UBERON:0002167	93.73	gold quality
superficial temporal artery	UBERON:0001614	93.72	gold quality
epithelial cell of pancreas	CL:0000083	93.64	gold quality
ectocervix	UBERON:0012249	93.59	gold quality
uterine cervix	UBERON:0000002	93.58	gold quality
endocervix	UBERON:0000458	93.55	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.20

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

120 targeting TENT2, 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-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-3134	100.00	66.43	777
HSA-MIR-3689D	100.00	66.14	1181
HSA-MIR-6851-5P	100.00	65.63	1294
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-4534	99.99	66.58	1907
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-19A-3P	99.98	75.33	2762
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-MIR-539-3P	99.98	70.74	1616
HSA-MIR-485-3P	99.98	70.68	1585
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-551B-5P	99.96	71.28	3493
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-548AT-5P	99.96	70.83	2666
HSA-MIR-3912-5P	99.95	66.11	925
HSA-MIR-8082	99.95	67.27	1170
HSA-MIR-6753-3P	99.93	66.57	637
HSA-MIR-7107-3P	99.93	66.73	627

Literature-anchored findings (GeneRIF, showing 12)

• The authors show that the human CPEB1 can repress the activity of the reporter construct containing the HPV-16 early sequences. This repression can be counteracted by a human cytoplasmic poly(A) polymerase, hGLD-2 fused to CPEB1. (PMID:20144904)
• human CPE-binding protein 1 and hGLD-2 are antagonizing factors regulating p53 mRNA stability. (PMID:21995630)
• poly(A) polymerase Gld2, deadenylase PARN, and translation inhibitory factor neuroguidin (Ngd) are components of a dendritic CPEB-associated polyadenylation apparatus (PMID:22727665)
• Study identified TUT7, TUT4, and TUT2 as novel components of the miRNA biogenesis pathway. (PMID:23063654)
• The noncanonical polymerase Gld2 has been implicated in the stabilization of miR-122, possibly through catalyzing 3’ monoadenylation (PMID:23200856)
• HBx is a critical protein derived from HBV, which regulates miR-122 via down-regulating Gld2 (PMID:24667324)
• QKI-7 recruits PAPD4 to regulate post-transcriptional polyadenylation of target mRNAs. (PMID:26926106)
• our results propose a novel feedback regulatory mechanism for controlling HCV RNA abundance by the viral capsid protein, which is capable of modulating miR-122 activity and stability through the inhibition of GLD-2. (PMID:27366906)
• The data demonstrate a novel phosphorylation-dependent mechanism to regulate Gld2 activity, revealing tumour suppressor miRNAs(miR-122) as a previously unknown target of Akt1-dependent signalling (PMID:31057087)
• The RNA-binding protein QKI-7 recruits the poly(A) polymerase GLD-2 for 3’ adenylation and selective stabilization of microRNA-122. (PMID:31792053)
• DDX6 is a positive regulator of Ataxin-2/PAPD4 cytoplasmic polyadenylation machinery. (PMID:33756349)
• TENT2, TUT4, and TUT7 selectively regulate miRNA sequence and abundance. (PMID:36071058)

Cross-species orthologs

8 orthologs

Organism	Symbol	Gene ID
danio_rerio	tent2	ENSDARG00000099679
mus_musculus	Tent2	ENSMUSG00000042167
rattus_norvegicus	Tent2	ENSRNOG00000012099
drosophila_melanogaster	mkg-p	FBGN0035889
drosophila_melanogaster	Tailor	FBGN0037470
drosophila_melanogaster	Gld2	FBGN0038934
drosophila_melanogaster	wisp	FBGN0260780
caenorhabditis_elegans	gldr-2	WBGENE00009284

Paralogs (4): TUT7 (ENSG00000083223), MTPAP (ENSG00000107951), TUT4 (ENSG00000134744), TUT1 (ENSG00000149016)

Protein

Protein identifiers

Poly(A) RNA polymerase GLD2 — Q6PIY7 (reviewed: Q6PIY7)

Alternative names: PAP-associated domain-containing protein 4, Terminal nucleotidyltransferase 2, Terminal uridylyltransferase 2

All UniProt accessions (2): Q6PIY7, D6RAF2

UniProt curated annotations — full annotation on UniProt →

Function. Cytoplasmic poly(A) RNA polymerase that adds successive AMP monomers to the 3’-end of specific RNAs, forming a poly(A) tail. In contrast to the canonical nuclear poly(A) RNA polymerase, it only adds poly(A) to selected cytoplasmic mRNAs. Does not play a role in replication-dependent histone mRNA degradation. Adds a single nucleotide to the 3’ end of specific miRNAs, monoadenylation stabilizes and prolongs the activity of some but not all miRNAs.

Subunit / interactions. Interacts with CPEB1, CPEB2, CPSF1 and PABPC1. Interacts with QKI isoform QKI7; promoting recruitment to miRNA miR-122 and miR-122 stabilization.

Subcellular location. Cytoplasm. Nucleus.

Tissue specificity. Expressed in brain. Within brain, it is expressed in cerebellum, hippocampus and medulla.

Similarity. Belongs to the DNA polymerase type-B-like family. GLD2 subfamily.

Isoforms (2)

UniProt ID	Names	Canonical?
Q6PIY7-1	1	yes
Q6PIY7-2	2

RefSeq proteins (56): NP_001107865, NP_001107866, NP_001284673, NP_001284674, NP_001336477, NP_001336478, NP_001336479, NP_001336480, NP_001336481, NP_001336482, NP_001336483, NP_001375022, NP_001375023, NP_001375024, NP_001375025, NP_001375026, NP_001375027, NP_001375028, NP_001375029, NP_001375030, NP_001375031, NP_001375032, NP_001375034, NP_001375035, NP_001375036, NP_001375037, NP_001375038, NP_001375039, NP_001375040, NP_001375041, NP_001375042, NP_001375043, NP_001375044, NP_001375045, NP_001375046, NP_001375047, NP_001375048, NP_001375049, NP_001375050, NP_001375051, NP_001375052, NP_001375053, NP_001375054, NP_001375055, NP_001375056, NP_001375057, NP_001375058, NP_001375059, NP_001375060, NP_001375061, NP_001375062, NP_001375063, NP_001375064, NP_001375065, NP_001375066, NP_776158 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002058	PAP_assoc	Domain
IPR043519	NT_sf	Homologous_superfamily
IPR054708	MTPAP-like_central	Domain

Pfam: PF03828, PF22600

Enzyme classification (BRENDA):

• EC 2.7.7.19 — polynucleotide adenylyltransferase (BRENDA: 35 organisms, 181 substrates, 125 inhibitors, 114 Km, 53 kcat entries)

Substrate kinetics (BRENDA)

19 substrates with measured Km, best-characterized 15. Km ranges are aggregated across organisms/conditions.

Substrate	Km (mM)	Measurements
ATP	0.028–2.191	54
RNA (A)15	0.51–24.99	23
CTP	0.1036–4.7	7
(A)N	0.0468–0.711	5
OLIGO(A)14	0.0005–0.037	5
(A)15	0.0009–0.0053	3
GTP	0.055–0.062	2
OLIGO(A)18	0.0468–0.0642	2
OLIGO(A)N	0.01–0.3	2
2-AMINOPURINE RIBOSIDE TRIPHOSPHATE	0.0197	1
DATP	0.06	1
OLIGO(A)12	0.0004	1
OLIGO(A)17C	0.0263	1
OLIGOADENYLATE	0.2	1
POLY(A)N	0.0036	1

Catalyzed reactions (Rhea), 1 shown:

• RNA(n) + ATP = RNA(n)-3’-adenine ribonucleotide + diphosphate (RHEA:11332)

UniProt features (13 total): modified residue 3, binding site 2, chain 1, domain 1, splice variant 1, mutagenesis site 1, sequence conflict 1, region of interest 1, short sequence motif 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6PIY7-F1	76.69	0.62

Functional residue map

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

Ligand- & substrate-binding residues (2): 213; 215

Post-translational modifications (3): 62, 69, 95

Mutagenesis-validated functional residues (1):

Position	Phenotype
215	catalytically inactive.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 210 (showing top): GOBP_HEMATOPOIETIC_PROGENITOR_CELL_DIFFERENTIATION, TGCGCANK_UNKNOWN, GAANYNYGACNY_UNKNOWN, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GAUSSMANN_MLL_AF4_FUSION_TARGETS_C_UP, GOBP_POST_TRANSCRIPTIONAL_REGULATION_OF_GENE_EXPRESSION, MILI_PSEUDOPODIA_HAPTOTAXIS_UP, GOBP_REGULATION_OF_CATABOLIC_PROCESS, GOBP_MRNA_3_END_PROCESSING, TGTTTAC_MIR30A5P_MIR30C_MIR30D_MIR30B_MIR30E5P, GOCC_RNA_POLYMERASE_COMPLEX, GOBP_HISTONE_MRNA_METABOLIC_PROCESS, GOBP_HISTONE_MRNA_CATABOLIC_PROCESS, TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_16D_DN

GO Biological Process (8): hematopoietic progenitor cell differentiation (GO:0002244), RNA 3’-end processing (GO:0031123), mRNA 3’-end processing (GO:0031124), histone mRNA catabolic process (GO:0071044), target-directed miRNA degradation (GO:0140958), negative regulation of miRNA catabolic process (GO:2000626), mRNA processing (GO:0006397), regulation of gene expression (GO:0010468)

GO Molecular Function (7): ATP binding (GO:0005524), metal ion binding (GO:0046872), poly(A) RNA polymerase activity (GO:1990817), nucleotide binding (GO:0000166), protein binding (GO:0005515), transferase activity (GO:0016740), nucleotidyltransferase activity (GO:0016779)

GO Cellular Component (3): cytoplasm (GO:0005737), nuclear RNA-directed RNA polymerase complex (GO:0031380), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
RNA processing	2
miRNA catabolic process	2
hemopoiesis	1
cell differentiation	1
mRNA processing	1
RNA 3’-end processing	1
nuclear-transcribed mRNA catabolic process	1
histone mRNA metabolic process	1
post-transcriptional gene silencing	1
negative regulation of miRNA-mediated gene silencing	1
negative regulation of RNA catabolic process	1
regulation of miRNA catabolic process	1
negative regulation of miRNA metabolic process	1
mRNA metabolic process	1
gene expression	1
regulation of macromolecule biosynthetic process	1
adenyl ribonucleotide binding	1
purine ribonucleoside triphosphate binding	1
cation binding	1
adenylyltransferase activity	1
nucleoside phosphate binding	1
heterocyclic compound binding	1
binding	1
catalytic activity	1
transferase activity, transferring phosphorus-containing groups	1
intracellular anatomical structure	1
cellular anatomical structure	1
RNA-directed RNA polymerase complex	1
nuclear protein-containing complex	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

802 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TENT2	CPEB1	Q9BZB8	981
TENT2	SYMPK	Q92797	974
TENT2	PARN	O95453	905
TENT2	PNLDC1	Q8NA58	883
TENT2	PAPOLA	P51003	867
TENT2	PAPOLG	Q9BWT3	867
TENT2	PAPOLB	Q9NRJ5	867
TENT2	NGDN	Q8NEJ9	861
TENT2	PABPC1L	Q4VXU2	719
TENT2	DIS3L2	Q8IYB7	632
TENT2	CPEB4	Q17RY0	627
TENT2	XRN2	Q9H0D6	619
TENT2	CPEB2	Q7Z5Q1	608
TENT2	FBF1	Q8TES7	582
TENT2	DICER1	Q9UPY3	562

IntAct

28 interactions, top by confidence:

A	B	Type	Score
CALCOCO2	TENT2	psi-mi:“MI:0915”(physical association)	0.560
TENT2	RBPMS	psi-mi:“MI:0915”(physical association)	0.560
TENT2	CALCOCO2	psi-mi:“MI:0915”(physical association)	0.560
RBPMS	TENT2	psi-mi:“MI:0915”(physical association)	0.560
KRTAP6-3	TENT2	psi-mi:“MI:0915”(physical association)	0.560
CADPS	TENT2	psi-mi:“MI:0915”(physical association)	0.560
TENT2	DTX2	psi-mi:“MI:0915”(physical association)	0.560
BCCIP	EIF6	psi-mi:“MI:0914”(association)	0.560
SOX2	CBX4	psi-mi:“MI:0914”(association)	0.350
HNRNPH1	VWA8	psi-mi:“MI:0914”(association)	0.350
ILF3	GTPBP10	psi-mi:“MI:0914”(association)	0.350
RBM4B	ZNF320	psi-mi:“MI:0914”(association)	0.350
AFG2A	ESYT2	psi-mi:“MI:0914”(association)	0.350
GPKOW	ESYT2	psi-mi:“MI:2364”(proximity)	0.270
QKI	SMCHD1	psi-mi:“MI:2364”(proximity)	0.270
DDX6	RPSA2	psi-mi:“MI:2364”(proximity)	0.270
TENT2	KRTAP6-3	psi-mi:“MI:0915”(physical association)	0.000
TENT2	CADPS	psi-mi:“MI:0915”(physical association)	0.000
DTX2	TENT2	psi-mi:“MI:0915”(physical association)	0.000
sdhA	TENT2	psi-mi:“MI:0915”(physical association)	0.000
hutU	TENT2	psi-mi:“MI:0915”(physical association)	0.000
TENT2	ilvE	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (49): PAPD4 (Two-hybrid), PAPD4 (Two-hybrid), PAPD4 (Affinity Capture-MS), PAPD4 (Two-hybrid), PAPD4 (Affinity Capture-MS), PAPD4 (Affinity Capture-MS), PAPD4 (Affinity Capture-MS), PAPD4 (Two-hybrid), PAPD4 (Affinity Capture-MS), PAPD4 (Proximity Label-MS), PAPD4 (Affinity Capture-Western), PAPD4 (Two-hybrid), PAPD4 (Two-hybrid), KRTAP6-3 (Two-hybrid), PAPD4 (Protein-RNA)

ESM2 similar proteins: A0A0R4IXF6, A9JRL3, O08537, O15164, O46102, O74326, O75925, O88907, O93511, P06212, P19785, P45446, Q0VFA3, Q1LUC3, Q2HJ44, Q503I9, Q5R4L1, Q5U315, Q5XET5, Q5ZLG9, Q61083, Q62986, Q64127, Q641A1, Q68ED3, Q69Z98, Q6DD21, Q6DFA8, Q6PCL9, Q6PIY7, Q8C0M0, Q8N264, Q8NDF8, Q91250, Q91738, Q91YI6, Q92731, Q95171, Q9BWT3, Q9D0D3

Diamond homologs: B2RX14, D2HS90, O13833, O17087, O64642, Q0VFA3, Q1JPD6, Q2HJ44, Q3MHT4, Q503I9, Q5BLK4, Q5TAX3, Q5U315, Q5VYS8, Q641A1, Q6DFA8, Q6PIY7, Q8R3F9, Q91YI6, Q9H6E5, Q9UT49, Q9VD44, O74326, Q5XET5, Q9VYS4, A9JTS5, Q4KMD7, Q8WQX6, Q9UTN3, O13798, Q8WQX5, Q381M1, Q7KVS9, Q9D0D3, Q9NVV4

SIGNOR signaling

5 interactions.

A	Effect	B	Mechanism
PRKACA	“down-regulates activity”	TENT2	phosphorylation
PRKACB	“down-regulates activity”	TENT2	phosphorylation
PRKACG	“down-regulates activity”	TENT2	phosphorylation
AKT1	“down-regulates activity”	TENT2	phosphorylation
PKA	“down-regulates activity”	TENT2	phosphorylation

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	64
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
814693	GRCh37/hg19 5q13.2-15(chr5:72790061-97478870)x3	Pathogenic

SpliceAI

3479 predictions. Top by Δscore:

Variant	Effect	Δscore
5:79619608:CTA:C	acceptor_loss	1.0000
5:79619609:TA:T	acceptor_loss	1.0000
5:79619611:G:GC	acceptor_loss	1.0000
5:79619781:GCAGA:G	donor_gain	1.0000
5:79619784:GA:G	donor_gain	1.0000
5:79619786:G:GG	donor_gain	1.0000
5:79619992:A:AG	acceptor_gain	1.0000
5:79619992:AGCTT:A	acceptor_gain	1.0000
5:79619993:G:GT	acceptor_gain	1.0000
5:79619993:GC:G	acceptor_gain	1.0000
5:79619993:GCT:G	acceptor_gain	1.0000
5:79619993:GCTT:G	acceptor_gain	1.0000
5:79619993:GCTTG:G	acceptor_gain	1.0000
5:79620079:AGGAA:A	donor_gain	1.0000
5:79620080:GGAA:G	donor_gain	1.0000
5:79620080:GGAAG:G	donor_gain	1.0000
5:79620081:GAA:G	donor_gain	1.0000
5:79620081:GAAG:G	donor_gain	1.0000
5:79620081:GAAGT:G	donor_loss	1.0000
5:79620082:AA:A	donor_gain	1.0000
5:79620083:AGTA:A	donor_loss	1.0000
5:79620084:G:GG	donor_gain	1.0000
5:79620085:T:G	donor_loss	1.0000
5:79640841:T:TA	acceptor_gain	1.0000
5:79640966:G:GG	donor_gain	1.0000
5:79645117:TTTCA:T	acceptor_loss	1.0000
5:79645118:TTCAG:T	acceptor_loss	1.0000
5:79645121:A:AG	acceptor_gain	1.0000
5:79645121:AGC:A	acceptor_gain	1.0000
5:79645121:AGCG:A	acceptor_gain	1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000036095 (5:79655863 T>C), RS1000036941 (5:79678460 A>G), RS1000068456 (5:79678491 T>TA), RS1000074098 (5:79641331 A>G), RS1000142749 (5:79677883 T>C), RS1000162974 (5:79612967 A>C,T), RS1000191549 (5:79662001 G>GA), RS1000227496 (5:79654385 T>C,G), RS1000227541 (5:79613428 A>C), RS1000254406 (5:79661027 T>C), RS1000368353 (5:79625805 A>G), RS1000420705 (5:79626026 A>G), RS1000516606 (5:79684607 A>G), RS1000531761 (5:79632730 AGTTAT>A), RS1000535216 (5:79659915 C>T)

Disease associations

OMIM: gene MIM:614121 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

15 associations (top):

Study	Trait	p-value
GCST001122_1	Adiponectin levels	5.000000e-06
GCST003265_192	Post bronchodilator FEV1/FVC ratio in COPD	2.000000e-06
GCST003265_193	Post bronchodilator FEV1/FVC ratio in COPD	2.000000e-06
GCST003265_194	Post bronchodilator FEV1/FVC ratio in COPD	2.000000e-06
GCST003265_195	Post bronchodilator FEV1/FVC ratio in COPD	2.000000e-06
GCST003265_196	Post bronchodilator FEV1/FVC ratio in COPD	2.000000e-06
GCST003265_197	Post bronchodilator FEV1/FVC ratio in COPD	3.000000e-06
GCST003265_341	Post bronchodilator FEV1/FVC ratio in COPD	2.000000e-06
GCST003265_342	Post bronchodilator FEV1/FVC ratio in COPD	2.000000e-06
GCST003265_343	Post bronchodilator FEV1/FVC ratio in COPD	2.000000e-06
GCST003265_344	Post bronchodilator FEV1/FVC ratio in COPD	3.000000e-06
GCST003265_345	Post bronchodilator FEV1/FVC ratio in COPD	3.000000e-06
GCST003265_346	Post bronchodilator FEV1/FVC ratio in COPD	3.000000e-06
GCST003265_347	Post bronchodilator FEV1/FVC ratio in COPD	3.000000e-06
GCST009856_30	Leukocyte telomere length	2.000000e-06

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004502	adiponectin measurement
EFO:0004713	FEV/FVC ratio

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

18 total (human), top 18 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	affects methylation, increases stability, affects expression	3
trichostatin A	affects cotreatment, increases expression	2
FR900359	decreases phosphorylation	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
jinfukang	decreases expression	1
Arsenic Trioxide	increases expression	1
Acetaminophen	decreases expression	1
Demecolcine	increases expression	1
Hydrogen Peroxide	affects expression	1
Valproic Acid	decreases expression	1
Vincristine	increases expression	1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	1
Aflatoxin B1	increases methylation	1
Cadmium Chloride	decreases expression	1
Copper Sulfate	increases expression	1
tert-Butylhydroperoxide	affects expression	1
Vitamin K 3	affects expression	1

Clinical trials (associated diseases)

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