LSM5

Summary

LSM5 (LSM5 homolog, U6 small nuclear RNA and mRNA degradation associated, HGNC:17162) is a protein-coding gene on chromosome 7p14.3, encoding U6 snRNA-associated Sm-like protein LSm5 (Q9Y4Y9). Plays a role in pre-mRNA splicing as component of the U4/U6-U5 tri-snRNP complex that is involved in spliceosome assembly, and as component of the precatalytic spliceosome (spliceosome B complex). It is a common-essential gene (DepMap: required in 98.3% of cancer cell lines).

Sm-like proteins were identified in a variety of organisms based on sequence homology with the Sm protein family (see SNRPD2; MIM 601061). Sm-like proteins contain the Sm sequence motif, which consists of 2 regions separated by a linker of variable length that folds as a loop. The Sm-like proteins are thought to form a stable heteromer present in tri-snRNP particles, which are important for pre-mRNA splicing.

Source: NCBI Gene 23658 — RefSeq curated summary.

At a glance

• GWAS associations: 6
• Clinical variants (ClinVar): 10 total
• Cancer dependency (DepMap): dependent in 98.3% of screened cell lines (common-essential)
• MANE Select transcript: NM_012322

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:17162
Approved symbol	LSM5
Name	LSM5 homolog, U6 small nuclear RNA and mRNA degradation associated
Location	7p14.3
Locus type	gene with protein product
Status	Approved
Aliases	YER146W
Ensembl gene	ENSG00000106355
Ensembl biotype	protein_coding
OMIM	607285
Entrez	23658

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 10 protein_coding, 2 retained_intron, 1 nonsense_mediated_decay

ENST00000223084, ENST00000409292, ENST00000409782, ENST00000409909, ENST00000409952, ENST00000409987, ENST00000410044, ENST00000450169, ENST00000468872, ENST00000480956, ENST00000935374, ENST00000935375, ENST00000935376

RefSeq mRNA: 3 — MANE Select: NM_012322 NM_001130710, NM_001139499, NM_012322

CCDS: CCDS47571, CCDS5438

Canonical transcript exons

ENST00000450169 — 5 exons

Exon	Start	End
ENSE00001682291	32485338	32487293
ENSE00003465829	32487685	32487757
ENSE00003493673	32488625	32488652
ENSE00003549106	32490320	32490380
ENSE00003565188	32489249	32489344

Expression profiles

Bgee: expression breadth ubiquitous, 294 present calls, max score 97.62.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 27.9520 / max 605.1031, expressed in 1800 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
83492	24.7358	1794
83493	3.2162	1501

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
ventricular zone	UBERON:0003053	97.62	gold quality
ganglionic eminence	UBERON:0004023	97.44	gold quality
embryo	UBERON:0000922	97.28	gold quality
penis	UBERON:0000989	96.41	gold quality
rectum	UBERON:0001052	96.21	gold quality
superior surface of tongue	UBERON:0007371	96.05	gold quality
mucosa of transverse colon	UBERON:0004991	95.99	gold quality
body of pancreas	UBERON:0001150	95.89	gold quality
pylorus	UBERON:0001166	95.75	gold quality
jejunum	UBERON:0002115	95.75	gold quality
bone marrow	UBERON:0002371	95.64	gold quality
synovial joint	UBERON:0002217	95.54	gold quality
body of tongue	UBERON:0011876	95.44	gold quality
pharyngeal mucosa	UBERON:0000355	95.43	gold quality
cardia of stomach	UBERON:0001162	95.35	gold quality
jejunal mucosa	UBERON:0000399	95.34	gold quality
lymph node	UBERON:0000029	95.30	gold quality
tongue	UBERON:0001723	95.20	gold quality
trabecular bone tissue	UBERON:0002483	95.17	gold quality
urethra	UBERON:0000057	95.10	gold quality
mucosa of sigmoid colon	UBERON:0004993	95.08	gold quality
oral cavity	UBERON:0000167	95.01	gold quality
colonic mucosa	UBERON:0000317	95.00	gold quality
mammalian vulva	UBERON:0000997	94.96	gold quality
pancreas	UBERON:0001264	94.84	gold quality
nasal cavity mucosa	UBERON:0001826	94.83	gold quality
islet of Langerhans	UBERON:0000006	94.82	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	94.82	gold quality
mucosa of paranasal sinus	UBERON:0005030	94.80	gold quality
endometrium	UBERON:0001295	94.78	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-HCAD-1	yes	41.88
E-GEOD-125970	yes	25.37
E-ANND-3	yes	11.12
E-MTAB-9388	no	12.20

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

84 targeting LSM5, 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-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-6873-3P	100.00	71.42	2626
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-8068	99.98	73.85	2376
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-548N	99.98	71.94	4170
HSA-LET-7F-2-3P	99.98	70.98	2588
HSA-MIR-1185-1-3P	99.98	71.04	2593
HSA-MIR-1185-2-3P	99.98	71.04	2593
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-493-5P	99.96	72.47	2382
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-6508-5P	99.92	70.67	2465
HSA-MIR-7-1-3P	99.91	71.53	4384
HSA-MIR-7-2-3P	99.91	71.40	4394
HSA-MIR-10527-5P	99.91	72.28	3754
HSA-MIR-8063	99.91	69.76	3146
HSA-MIR-3671	99.90	73.04	3897
HSA-MIR-221-5P	99.86	65.45	1052
HSA-MIR-8073	99.86	65.21	1118
HSA-MIR-8067	99.86	69.59	2260

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 98.3% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 1)

• LSm1-7 proteins colocalize with DCP1,DCP2 and Xrn1 in cytoplasmic foci (PMID:12515382)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	lsm5	ENSDARG00000071573
mus_musculus	Lsm5	ENSMUSG00000091625
rattus_norvegicus	Lsm5	ENSRNOG00000027305
drosophila_melanogaster	CG6610	FBGN0035675
caenorhabditis_elegans		WBGENE00003079

Protein

Protein identifiers

U6 snRNA-associated Sm-like protein LSm5 — Q9Y4Y9 (reviewed: Q9Y4Y9)

All UniProt accessions (4): Q9Y4Y9, A0A090N8Y5, B8ZZF8, F8W8Y8

UniProt curated annotations — full annotation on UniProt →

Function. Plays a role in pre-mRNA splicing as component of the U4/U6-U5 tri-snRNP complex that is involved in spliceosome assembly, and as component of the precatalytic spliceosome (spliceosome B complex). The heptameric LSM2-8 complex binds specifically to the 3’-terminal U-tract of U6 snRNA.

Subunit / interactions. Component of the precatalytic spliceosome (spliceosome B complex). Component of the U4/U6-U5 tri-snRNP complex, a building block of the precatalytic spliceosome (spliceosome B complex). The U4/U6-U5 tri-snRNP complex is composed of the U4, U6 and U5 snRNAs and at least PRPF3, PRPF4, PRPF6, PRPF8, PRPF31, SNRNP200, TXNL4A, SNRNP40, SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF, SNRPG, DDX23, CD2BP2, PPIH, SNU13, EFTUD2, SART1 and USP39, plus LSM2, LSM3, LSM4, LSM5, LSM6, LSM7 and LSM8. LSM2, LSM3, LSM4, LSM5, LSM6, LSM7 and LSM8 form a heptameric, ring-shaped subcomplex (the LSM2-8 complex) that is part of the U4/U6-U5 tri-snRNP complex and the precatalytic spliceosome.

Subcellular location. Nucleus.

Similarity. Belongs to the snRNP Sm proteins family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9Y4Y9-1	1	yes
Q9Y4Y9-2	2

RefSeq proteins (3): NP_001124182, NP_001132971, NP_036454* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001163	Sm_dom_euk/arc	Domain
IPR010920	LSM_dom_sf	Homologous_superfamily
IPR033871	LSm5	Domain
IPR047575	Sm	Domain

Pfam: PF01423

UniProt features (5 total): initiator methionine 1, chain 1, domain 1, modified residue 1, splice variant 1

Structure

Experimental structures (PDB)

20 structures.

PDB	Method	Resolution (Å)
8H6L	ELECTRON MICROSCOPY	2.6
8H6K	ELECTRON MICROSCOPY	2.7
6QW6	ELECTRON MICROSCOPY	2.92
8H6E	ELECTRON MICROSCOPY	3.2
8H6J	ELECTRON MICROSCOPY	3.25
6QX9	ELECTRON MICROSCOPY	3.28
6AHD	ELECTRON MICROSCOPY	3.8
8QZS	ELECTRON MICROSCOPY	4.1
8R09	ELECTRON MICROSCOPY	4.3
8R0B	ELECTRON MICROSCOPY	4.4
5O9Z	ELECTRON MICROSCOPY	4.5
8QO9	ELECTRON MICROSCOPY	5.29
6AH0	ELECTRON MICROSCOPY	5.7
8R0A	ELECTRON MICROSCOPY	5.8
8R08	ELECTRON MICROSCOPY	6.1
8RM5	ELECTRON MICROSCOPY	6.9
3JCR	ELECTRON MICROSCOPY	7
7ABG	ELECTRON MICROSCOPY	7.8
9R8V	ELECTRON MICROSCOPY	8.5
8QXD	ELECTRON MICROSCOPY	9.6

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9Y4Y9-F1	91.28	0.84

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): 2

Function

Pathways and Gene Ontology

Reactome pathways

6 pathways

ID	Pathway
R-HSA-430039	mRNA decay by 5’ to 3’ exoribonuclease
R-HSA-72163	mRNA Splicing - Major Pathway
R-HSA-429914	Deadenylation-dependent mRNA decay
R-HSA-72172	mRNA Splicing
R-HSA-72203	Processing of Capped Intron-Containing Pre-mRNA
R-HSA-8953854	Metabolism of RNA

MSigDB gene sets: 221 (showing top): GOBP_REGULATION_OF_MRNA_CATABOLIC_PROCESS, MODULE_151, REACTOME_MRNA_DECAY_BY_5_TO_3_EXORIBONUCLEASE, DITTMER_PTHLH_TARGETS_UP, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, PUJANA_CHEK2_PCC_NETWORK, GOBP_POST_TRANSCRIPTIONAL_REGULATION_OF_GENE_EXPRESSION, MUELLER_PLURINET, GOBP_SPLICEOSOMAL_TRI_SNRNP_COMPLEX_ASSEMBLY, GOBP_REGULATION_OF_CATABOLIC_PROCESS, GOBP_POSITIVE_REGULATION_OF_CATABOLIC_PROCESS, GAZDA_DIAMOND_BLACKFAN_ANEMIA_PROGENITOR_DN, BLALOCK_ALZHEIMERS_DISEASE_UP, REACTOME_PROCESSING_OF_CAPPED_INTRON_CONTAINING_PRE_MRNA, GOBP_PROTEIN_RNA_COMPLEX_ORGANIZATION

GO Biological Process (5): mRNA splicing, via spliceosome (GO:0000398), mRNA processing (GO:0006397), mRNA catabolic process (GO:0006402), response to bacterium (GO:0009617), RNA splicing (GO:0008380)

GO Molecular Function (3): RNA binding (GO:0003723), protein heterodimerization activity (GO:0046982), protein binding (GO:0005515)

GO Cellular Component (11): nucleus (GO:0005634), nucleoplasm (GO:0005654), spliceosomal complex (GO:0005681), U6 snRNP (GO:0005688), cytoplasm (GO:0005737), cytosol (GO:0005829), U4/U6 x U5 tri-snRNP complex (GO:0046540), U2-type precatalytic spliceosome (GO:0071005), Lsm2-8 complex (GO:0120115), Lsm1-7-Pat1 complex (GO:1990726), ribonucleoprotein complex (GO:1990904)

Reactome top-level categories

Rollup of top-4 pathways:

Category	Pathways
Metabolism of RNA	2
Deadenylation-dependent mRNA decay	1
mRNA Splicing	1
Processing of Capped Intron-Containing Pre-mRNA	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
RNA processing	2
mRNA metabolic process	2
Sm-like protein family complex	2
RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	1
mRNA processing	1
RNA catabolic process	1
negative regulation of gene expression	1
response to other organism	1
nucleic acid binding	1
protein dimerization activity	1
binding	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
nuclear protein-containing complex	1
ribonucleoprotein complex	1
spliceosomal snRNP complex	1
Lsm2-8 complex	1
intracellular anatomical structure	1
cytoplasm	1
U5 snRNP	1
U4/U6 snRNP	1
spliceosomal tri-snRNP complex	1
U2-type spliceosomal complex	1
U1 snRNP	1
U2 snRNP	1
U4/U6 x U5 tri-snRNP complex	1
precatalytic spliceosome	1
protein-containing complex	1

Protein interactions and networks

STRING

1704 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LSM5	LSM7	Q9UK45	997
LSM5	LSM6	P62312	996
LSM5	LSM2	Q9Y333	994
LSM5	LSM3	P62310	991
LSM5	LSM4	Q9Y4Z0	987
LSM5	LSM8	O95777	984
LSM5	LSM1	O15116	965
LSM5	XRN1	Q8IZH2	916
LSM5	SNRPD2	P43330	872
LSM5	SNRPE	P08578	739
LSM5	SNRPD3	P43331	667
LSM5	SNRPD1	P13641	667
LSM5	PRPF38A	Q8NAV1	640
LSM5	LSM10	Q969L4	614
LSM5	LSM12	Q3MHD2	604

IntAct

99 interactions, top by confidence:

A	B	Type	Score
LSM1	LSM3	psi-mi:“MI:0915”(physical association)	0.950
LSM3	LSM1	psi-mi:“MI:0914”(association)	0.950
SNRPF	GEMIN2	psi-mi:“MI:0914”(association)	0.910
LSM6	LSM5	psi-mi:“MI:0915”(physical association)	0.900
LSM5	LSM7	psi-mi:“MI:0915”(physical association)	0.900
LSM5	LSM6	psi-mi:“MI:0915”(physical association)	0.900
LSM7	LSM5	psi-mi:“MI:0915”(physical association)	0.900
SNRPF	LSM5	psi-mi:“MI:0915”(physical association)	0.880
LSM5	SNRPF	psi-mi:“MI:0915”(physical association)	0.880
LSM1	LSM6	psi-mi:“MI:0914”(association)	0.840
LSM6	LSM1	psi-mi:“MI:0914”(association)	0.840
LSM3	LSM5	psi-mi:“MI:0915”(physical association)	0.800
LSM2	LSM8	psi-mi:“MI:0915”(physical association)	0.790

BioGRID (162): LSM5 (Two-hybrid), LSM5 (Two-hybrid), LSM7 (Two-hybrid), LSM2 (Co-fractionation), LSM3 (Co-fractionation), LSM4 (Co-fractionation), LSM6 (Co-fractionation), LSM7 (Co-fractionation), NAA38 (Co-fractionation), LSM5 (Synthetic Lethality), LSM5 (Two-hybrid), PATL1 (Affinity Capture-MS), POLH (Affinity Capture-MS), LSM5 (Affinity Capture-MS), ZNF511 (Affinity Capture-MS)

ESM2 similar proteins: A1CE19, A4RQ29, A5DRQ6, A6S5C9, A6ZYX7, A7F5M4, A7TK72, A7UXE4, A8NHT8, B6YUU5, C5A1H1, C6A1T2, O22823, O26745, O42978, O74016, P0CR24, P0CR25, P40089, P54999, P57670, P57743, P62322, Q06406, Q0UWI9, Q0W8R9, Q12330, Q12U30, Q1DRN0, Q1ZXD5, Q2HJH0, Q465S1, Q4PG71, Q54HF6, Q552U1, Q55EX5, Q5JIE0, Q5R628, Q6BR90, Q6CPS7

Diamond homologs: A1XQR9, A4FUI2, A8MWD9, A8XDT0, C6A1T2, O26745, P40089, P62303, P62304, P62305, P62322, Q0W8R9, Q12330, Q12U30, Q2HJH0, Q54RX0, Q5R628, Q7ZUG0, Q9FKB0, Q9N4G9, Q9USZ3, Q9VLV5, Q9VXE0, Q9XTU6, Q9Y4Y9, Q9YEQ5, P24715, P62308, P62309, Q3ZBL0, A1CE19, A1DM27, A4RQ29, A5DRQ6, A6R363, A6S5C9, A7F5M4, A7UXE4, A8NHT8, B0DWN3

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
LSM5	“form complex”	“U4/U6.U5 snRNP complex”	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 38 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
mRNA decay by 5’ to 3’ exoribonuclease	6	152.3×	1e-11
mRNA Splicing	12	43.9×	3e-16
Processing of Capped Intron-Containing Pre-mRNA	13	35.6×	3e-16
snRNP Assembly	5	35.2×	2e-06
mRNA Splicing - Major Pathway	16	29.1×	8e-19
Metabolism of RNA	14	19.4×	3e-14
CHD1 and CHD2 subfamily	5	18.1×	4e-05
mRNA Polyadenylation	6	17.6×	8e-06

GO biological processes:

GO term	Partners	Fold	FDR
spliceosomal snRNP assembly	10	152.9×	2e-18
mRNA splicing, via spliceosome	18	43.4×	1e-23
RNA splicing	9	20.9×	2e-08

Disease & clinical

Clinical variants and AI predictions

ClinVar

10 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

581 predictions. Top by Δscore:

Variant	Effect	Δscore
7:32487290:CCAG:C	acceptor_gain	1.0000
7:32487291:CAGC:C	acceptor_gain	1.0000
7:32487291:CAG:C	acceptor_gain	0.9900
7:32487294:C:CC	acceptor_gain	0.9900
7:32487756:CA:C	acceptor_gain	0.9900
7:32489224:C:CT	donor_gain	0.9900
7:32489247:A:AC	donor_gain	0.9900
7:32489248:C:CC	donor_gain	0.9900
7:32489251:A:AC	donor_gain	0.9900
7:32489252:C:CC	donor_gain	0.9900
7:32489287:T:TA	donor_gain	0.9900
7:32487758:C:CC	acceptor_gain	0.9800
7:32489293:T:C	donor_gain	0.9800
7:32489522:T:TA	donor_gain	0.9800
7:32487298:A:C	acceptor_gain	0.9700
7:32487753:TTTCA:T	acceptor_gain	0.9700
7:32490314:GATTA:G	donor_loss	0.9700
7:32490315:ATTAC:A	donor_loss	0.9700
7:32490316:TTA:T	donor_loss	0.9700
7:32490317:TA:T	donor_loss	0.9700
7:32490318:ACC:A	donor_loss	0.9700
7:32490319:CCT:C	donor_loss	0.9700
7:32487292:AGCT:A	acceptor_loss	0.9600
7:32487293:GCT:G	acceptor_loss	0.9600
7:32487294:C:CA	acceptor_loss	0.9600
7:32487295:T:A	acceptor_loss	0.9600
7:32490287:C:CA	donor_gain	0.9600
7:32489292:A:AC	donor_gain	0.9500
7:32487292:A:T	acceptor_gain	0.9400
7:32487755:TCA:T	acceptor_gain	0.9400

AlphaMissense

589 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
7:32487692:A:T	I79K	1.000
7:32487701:C:A	G76V	1.000
7:32487701:C:T	G76E	1.000
7:32487702:C:G	G76R	1.000
7:32487702:C:T	G76R	1.000
7:32487707:A:G	L74P	1.000
7:32487710:A:G	L73S	1.000
7:32488643:A:G	L51P	1.000
7:32489253:A:C	F46L	1.000
7:32489253:A:T	F46L	1.000
7:32489255:A:G	F46L	1.000
7:32489259:A:C	D44E	1.000
7:32489259:A:T	D44E	1.000
7:32489260:T:A	D44V	1.000
7:32489260:T:G	D44A	1.000
7:32489261:C:A	D44Y	1.000
7:32489261:C:G	D44H	1.000
7:32489262:A:C	F43L	1.000
7:32489262:A:T	F43L	1.000
7:32489264:A:G	F43L	1.000
7:32489266:C:T	G42E	1.000
7:32489278:C:A	G38V	1.000
7:32489278:C:T	G38D	1.000
7:32489279:C:A	G38C	1.000
7:32489279:C:G	G38R	1.000
7:32489279:C:T	G38S	1.000
7:32487289:A:T	V83D	0.999
7:32487692:A:C	I79R	0.999
7:32487701:C:G	G76A	0.999
7:32487707:A:T	L74Q	0.999

dbSNP variants (sampled 300 via entrez): RS1000046709 (7:32495555 G>A,T), RS1000120628 (7:32496910 A>G), RS1000913873 (7:32493211 CA>C), RS1001164177 (7:32486824 T>A), RS1001614530 (7:32488236 C>G), RS1001856438 (7:32486868 C>T), RS1002008335 (7:32493214 G>A,T), RS1002351460 (7:32486597 G>A), RS1002419321 (7:32485693 T>C,G), RS1002489219 (7:32492699 G>A,C), RS1002796989 (7:32486009 T>A,C), RS1002968489 (7:32497233 T>C), RS1003377569 (7:32495559 G>A,C,T), RS1003622633 (7:32485231 A>C), RS1003780989 (7:32491466 A>G)

Disease associations

OMIM: gene MIM:607285 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

6 associations (top):

Study	Trait	p-value
GCST001838_10	Palmitic acid (16:0) levels	1.000000e-06
GCST002361_3	Smooth-surface caries	8.000000e-06
GCST005951_156	Body mass index	3.000000e-08
GCST007044_17	Extremely high intelligence	5.000000e-08
GCST007565_166	Morning person	2.000000e-15
GCST010396_247	Gut microbiota (bacterial taxa, hurdle binary method)	5.000000e-06

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0004340	body mass index
EFO:0004337	intelligence
EFO:0008328	chronotype measurement
EFO:0007874	gut microbiome measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
bisphenol A	increases expression, decreases expression, affects cotreatment	3
sodium arsenite	decreases expression, increases abundance, increases expression	3
Tretinoin	decreases expression	2
Valproic Acid	affects expression, increases expression	2
Cyclosporine	decreases expression	2
bisphenol F	affects cotreatment, increases expression	1
dicrotophos	decreases expression	1
methylmercuric chloride	decreases expression	1
beta-lapachone	increases expression	1
arsenite	affects binding, increases reaction	1
methylparaben	decreases expression	1
cobaltous chloride	decreases expression	1
ochratoxin A	affects cotreatment, decreases expression	1
azoxystrobin	increases expression	1
pyrimidifen	increases expression	1
bisphenol S	affects cotreatment, increases expression	1
Sunitinib	increases expression	1
Vorinostat	increases expression	1
Air Pollutants	decreases expression, increases abundance	1
Arsenic	increases abundance, increases expression	1
Benzo(a)pyrene	increases methylation	1
Cisplatin	decreases expression	1
Citrinin	decreases expression, affects cotreatment	1
Dexamethasone	affects cotreatment, increases expression	1
Diethylstilbestrol	increases expression	1
Formaldehyde	decreases expression	1
Gold	decreases expression	1
Hydrogen Peroxide	affects expression	1
Indomethacin	affects cotreatment, increases expression	1
Ivermectin	decreases expression	1

Clinical trials (associated diseases)

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