LSM2

Summary

LSM2 (LSM2 homolog, U6 small nuclear RNA and mRNA degradation associated, HGNC:13940) is a protein-coding gene on chromosome 6p21.33, encoding U6 snRNA-associated Sm-like protein LSm2 (Q9Y333). 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 100.0% of cancer cell lines).

This gene encodes a member of the LSm family of RNA-binding proteins. LSm proteins form stable heteromers that bind specifically to the 3’-terminal oligo(U) tract of U6 snRNA and may play a role in pre-mRNA splicing by mediating U4/U6 snRNP formation. Pseudogenes of this gene are located on the short arm of chromosomes 6 and 19.

Source: NCBI Gene 57819 — RefSeq curated summary.

At a glance

• GWAS associations: 24
• Clinical variants (ClinVar): 7 total
• Cancer dependency (DepMap): dependent in 100.0% of screened cell lines (common-essential)
• MANE Select transcript: NM_021177

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13940
Approved symbol	LSM2
Name	LSM2 homolog, U6 small nuclear RNA and mRNA degradation associated
Location	6p21.33
Locus type	gene with protein product
Status	Approved
Aliases	G7b, YBL026W
Ensembl gene	ENSG00000204392
Ensembl biotype	protein_coding
OMIM	607282
Entrez	57819

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 8 protein_coding, 6 protein_coding_CDS_not_defined

ENST00000375661, ENST00000470083, ENST00000470086, ENST00000475835, ENST00000477182, ENST00000491421, ENST00000493387, ENST00000904318, ENST00000936482, ENST00000936483, ENST00000936484, ENST00000936485, ENST00000936486, ENST00000936487

RefSeq mRNA: 1 — MANE Select: NM_021177 NM_021177

CCDS: CCDS4722

Canonical transcript exons

ENST00000375661 — 5 exons

Exon	Start	End
ENSE00001893967	31806755	31806966
ENSE00003515187	31806075	31806142
ENSE00003587687	31797396	31797882
ENSE00003594532	31798477	31798507
ENSE00003613042	31797990	31798049

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 96.36.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 72.9609 / max 704.1652, expressed in 1821 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
72835	42.0662	1806
72833	27.4832	1809
72834	3.4116	1247

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
ventricular zone	UBERON:0003053	96.36	gold quality
ganglionic eminence	UBERON:0004023	96.09	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	95.96	gold quality
mucosa of transverse colon	UBERON:0004991	95.69	gold quality
body of uterus	UBERON:0009853	94.04	gold quality
endocervix	UBERON:0000458	93.72	gold quality
myometrium	UBERON:0001296	93.72	gold quality
left uterine tube	UBERON:0001303	93.64	gold quality
muscle layer of sigmoid colon	UBERON:0035805	93.62	gold quality
ectocervix	UBERON:0012249	93.51	gold quality
lymph node	UBERON:0000029	93.38	gold quality
islet of Langerhans	UBERON:0000006	93.37	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	93.36	gold quality
cortical plate	UBERON:0005343	93.35	gold quality
granulocyte	CL:0000094	93.22	gold quality
descending thoracic aorta	UBERON:0002345	93.17	gold quality
ascending aorta	UBERON:0001496	93.15	gold quality
thoracic aorta	UBERON:0001515	93.15	gold quality
right adrenal gland	UBERON:0001233	93.01	gold quality
spleen	UBERON:0002106	92.94	gold quality
left coronary artery	UBERON:0001626	92.84	gold quality
body of pancreas	UBERON:0001150	92.79	gold quality
right coronary artery	UBERON:0001625	92.75	gold quality
right ovary	UBERON:0002118	92.72	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	92.66	gold quality
placenta	UBERON:0001987	92.66	gold quality
popliteal artery	UBERON:0002250	92.63	gold quality
tibial artery	UBERON:0007610	92.63	gold quality
fallopian tube	UBERON:0003889	92.59	gold quality
uterine cervix	UBERON:0000002	92.54	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-GEOD-75367	yes	70.51
E-GEOD-125970	yes	22.19
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

33 targeting LSM2, 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-6758-5P	100.00	66.21	1470
HSA-MIR-6856-5P	100.00	65.47	1298
HSA-MIR-1297	99.91	73.41	3162
HSA-MIR-4731-5P	99.89	67.23	2537
HSA-MIR-548D-3P	99.87	70.67	4362
HSA-MIR-548BB-3P	99.86	70.58	4354
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-548AC	99.84	70.77	4351
HSA-MIR-548H-3P	99.84	70.80	4349
HSA-MIR-548Z	99.84	70.80	4349
HSA-MIR-26A-5P	99.78	73.52	2303
HSA-MIR-26B-5P	99.78	73.51	2305
HSA-MIR-4465	99.71	72.56	2096
HSA-MIR-6751-5P	99.56	64.99	1145
HSA-MIR-513C-5P	99.50	68.42	1730
HSA-MIR-514B-5P	99.50	68.19	1766
HSA-MIR-6803-5P	99.19	63.90	1026
HSA-MIR-548AS-3P	99.12	69.12	2294
HSA-MIR-3127-3P	98.94	67.34	1055
HSA-MIR-6756-3P	98.94	66.79	1104
HSA-MIR-4711-5P	98.89	68.00	965
HSA-MIR-3938	98.72	66.07	834
HSA-MIR-5572	98.55	65.84	970
HSA-MIR-6771-3P	98.20	66.53	971
HSA-MIR-6870-3P	98.08	65.10	692
HSA-MIR-6883-3P	97.97	67.35	643
HSA-MIR-7112-3P	97.67	68.77	948
HSA-MIR-6855-5P	97.51	66.03	830

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 100.0% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 4)

• LSm1-7 proteins colocalize with DCP1,DCP2 and Xrn1 in cytoplasmic foci (PMID:12515382)
• SNRPN is a key player in pancreatic adenocarcinoma cell growth; depletion of SNRPN led to S phase cell cycle arrest and apoptosis (PMID:26261020)
• LSM2 is associated with a poor prognosis and promotes cell proliferation, migration, and invasion in skin cutaneous melanoma. (PMID:37312186)
• The mechanism of LSM2 in the progression of live hepatocellular carcinoma was analyzed based on bioinformatics. (PMID:37612479)

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	smx5	ENSDARG00000070867
danio_rerio	LSM2	ENSDARG00000103066
mus_musculus	Lsm2	ENSMUSG00000007050
rattus_norvegicus	Lsm2	ENSRNOG00000048725
drosophila_melanogaster	CG10418	FBGN0036277
caenorhabditis_elegans		WBGENE00001808

Protein

Protein identifiers

U6 snRNA-associated Sm-like protein LSm2 — Q9Y333 (reviewed: Q9Y333)

Alternative names: Protein G7b, Small nuclear ribonuclear protein D homolog, snRNP core Sm-like protein Sm-x5

All UniProt accessions (1): Q9Y333

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.

RefSeq proteins (1): NP_067000* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001163	Sm_dom_euk/arc	Domain
IPR010920	LSM_dom_sf	Homologous_superfamily
IPR016654	U6_snRNA_Lsm2	Family
IPR047575	Sm	Domain

Pfam: PF01423

UniProt features (3 total): chain 1, domain 1, modified residue 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-Q9Y333-F1	94.69	0.92

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): 79

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: 216 (showing top): MORF_DNMT1, BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN, GOBP_REGULATION_OF_MRNA_CATABOLIC_PROCESS, PAL_PRMT5_TARGETS_UP, CHIANG_LIVER_CANCER_SUBCLASS_UNANNOTATED_DN, MORF_RRM1, REACTOME_MRNA_DECAY_BY_5_TO_3_EXORIBONUCLEASE, MORF_HDAC1, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, MORF_HDAC2, GOMF_GTPASE_BINDING, PRAMOONJAGO_SOX4_TARGETS_DN, GOBP_POST_TRANSCRIPTIONAL_REGULATION_OF_GENE_EXPRESSION, GOBP_SPLICEOSOMAL_TRI_SNRNP_COMPLEX_ASSEMBLY, GOBP_REGULATION_OF_CATABOLIC_PROCESS

GO Biological Process (5): spliceosomal tri-snRNP complex assembly (GO:0000244), mRNA splicing, via spliceosome (GO:0000398), mRNA catabolic process (GO:0006402), mRNA processing (GO:0006397), RNA splicing (GO:0008380)

GO Molecular Function (4): RNA binding (GO:0003723), U6 snRNA binding (GO:0017070), small GTPase binding (GO:0031267), protein binding (GO:0005515)

GO Cellular Component (14): P-body (GO:0000932), 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), precatalytic spliceosome (GO:0071011), catalytic step 2 spliceosome (GO:0071013), 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
mRNA metabolic process	2
RNA processing	2
U5 snRNP	2
spliceosomal complex	2
Sm-like protein family complex	2
spliceosomal snRNP assembly	1
RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	1
mRNA processing	1
RNA catabolic process	1
negative regulation of gene expression	1
nucleic acid binding	1
snRNA binding	1
GTPase binding	1
binding	1
cytoplasmic ribonucleoprotein granule	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
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
Prp19 complex	1
catalytic complex	1
protein-containing complex	1

Protein interactions and networks

STRING

1754 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LSM2	LSM8	O95777	999
LSM2	LSM3	P62310	999
LSM2	LSM7	Q9UK45	998
LSM2	LSM6	P62312	996
LSM2	LSM5	Q9Y4Y9	994
LSM2	LSM1	O15116	986
LSM2	XRN1	Q8IZH2	936
LSM2	SNRPD2	P43330	922
LSM2	LSM4	Q9Y4Z0	902
LSM2	POLR2G	P52433	815
LSM2	SART3	Q15020	788
LSM2	LSM14A	Q8ND56	719
LSM2	SNRPD1	P13641	710
LSM2	SNRPD3	P43331	691
LSM2	SNRPE	P08578	667

IntAct

278 interactions, top by confidence:

A	B	Type	Score
LSM2	LSM3	psi-mi:“MI:0915”(physical association)	0.980
LSM3	LSM2	psi-mi:“MI:0915”(physical association)	0.980
LSM3	LSM2	psi-mi:“MI:2364”(proximity)	0.980

BioGRID (301): LSM2 (Two-hybrid), LSM2 (Two-hybrid), LSM2 (Two-hybrid), LSM2 (Two-hybrid), LSM2 (Two-hybrid), LSM2 (Two-hybrid), LSM2 (Two-hybrid), LSM2 (Two-hybrid), LSM2 (Two-hybrid), LNX1 (Two-hybrid), LSM8 (Two-hybrid), LSM3 (Two-hybrid), LSM7 (Two-hybrid), LSM2 (Two-hybrid), LSM1 (Co-fractionation)

ESM2 similar proteins: A0A324, A1XQR9, A4FUI2, A5JSS2, A6MZM2, G1SHQ2, O09167, O14602, O35900, O60739, P20280, P25800, P41567, P46778, P47813, P48024, P49666, P51971, P61220, P62303, P62304, P62305, P62308, P62309, Q09028, Q0D5W6, Q0P5B3, Q2KIA3, Q3B8H4, Q3ZBL0, Q4R4X9, Q503U0, Q5E938, Q5RA42, Q5RBW7, Q5RFF4, Q60872, Q60972, Q6GVM3, Q6QN05

Diamond homologs: A9CTE0, O35900, O94408, P38203, Q1H595, Q54TF6, Q8SQK1, Q9Y333, F4K4E3, O14352, O44437, O59734, P40070, P43321, P62306, P62307, P62321, Q17348, Q19952, Q24297, Q3T0Z8, Q3ZBK6, Q43582, Q54KX4, Q552U1, Q55EX5, Q8QZX5, Q969L4, Q9LGE6, Q9LM92, Q9QXA5, Q9S7E6, Q9SUM2, Q9Y4Z0, Q9ZRU9, Q02260, Q54F84, A5DRQ6, A6S5C9, A7F5M4

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
LSM2	“form complex”	“U4/U6.U5 snRNP complex”	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 71 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	7	98.7×	6e-11
Metabolism of non-coding RNA	5	58.7×	5e-07
SARS-CoV-2 modulates host translation machinery	7	29.0×	1e-07
snRNP Assembly	7	27.4×	2e-07
mRNA Splicing	10	20.3×	4e-09
Processing of Capped Intron-Containing Pre-mRNA	10	15.2×	4e-08
SARS-CoV-2-host interactions	6	13.2×	2e-04
mRNA Splicing - Major Pathway	12	12.1×	1e-08

GO biological processes:

GO term	Partners	Fold	FDR
spliceosomal snRNP assembly	8	68.4×	4e-11
RNA splicing, via transesterification reactions	5	45.9×	6e-06
mRNA splicing, via spliceosome	15	20.2×	2e-13
RNA splicing	11	14.3×	3e-08
mRNA processing	8	9.3×	1e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

466 predictions. Top by Δscore:

Variant	Effect	Δscore
6:31797880:TAA:T	acceptor_gain	1.0000
6:31797883:C:CC	acceptor_gain	1.0000
6:31798048:TA:T	acceptor_gain	1.0000
6:31798050:C:CC	acceptor_gain	1.0000
6:31798518:C:CT	acceptor_gain	1.0000
6:31806751:CCACC:C	donor_loss	1.0000
6:31806752:CACC:C	donor_loss	1.0000
6:31797878:GATAA:G	acceptor_gain	0.9900
6:31797879:ATAA:A	acceptor_gain	0.9900
6:31797881:AA:A	acceptor_gain	0.9900
6:31797881:AAC:A	acceptor_loss	0.9900
6:31797883:C:T	acceptor_loss	0.9900
6:31797985:CTCA:C	donor_loss	0.9900
6:31797986:TCAC:T	donor_loss	0.9900
6:31797987:CA:C	donor_loss	0.9900
6:31797989:C:CT	donor_loss	0.9900
6:31798046:GATA:G	acceptor_gain	0.9900
6:31798049:AC:A	acceptor_loss	0.9900
6:31798050:C:A	acceptor_loss	0.9900
6:31798051:T:G	acceptor_loss	0.9900
6:31798519:A:T	acceptor_gain	0.9900
6:31806069:ACCT:A	donor_loss	0.9900
6:31806070:CCT:C	donor_loss	0.9900
6:31806072:TA:T	donor_loss	0.9900
6:31806123:T:C	acceptor_gain	0.9900
6:31806123:T:TC	acceptor_gain	0.9900
6:31806143:C:CC	acceptor_gain	0.9900
6:31806753:A:AC	donor_gain	0.9900
6:31806753:AC:A	donor_gain	0.9900
6:31806754:C:CC	donor_gain	0.9900

AlphaMissense

616 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
6:31797792:C:G	A85P	1.000
6:31797800:A:G	L82P	1.000
6:31797836:A:T	V70E	1.000
6:31797845:A:T	V67D	1.000
6:31797854:C:A	G64V	1.000
6:31797854:C:T	G64D	1.000
6:31797855:C:A	G64C	1.000
6:31797855:C:G	G64R	1.000
6:31797855:C:T	G64S	1.000
6:31797857:C:A	R63L	1.000
6:31797860:A:C	I62S	1.000
6:31797860:A:T	I62N	1.000
6:31797862:G:C	F61L	1.000
6:31797862:G:T	F61L	1.000
6:31797863:A:C	F61C	1.000
6:31797864:A:G	F61L	1.000
6:31797864:A:T	F61I	1.000
6:31797865:G:C	C60W	1.000
6:31797867:A:G	C60R	1.000
6:31798033:A:G	L40P	1.000
6:31798033:A:T	L40Q	1.000
6:31798041:G:C	N37K	1.000
6:31798041:G:T	N37K	1.000
6:31798045:A:G	L36P	1.000
6:31798481:T:A	D33V	1.000
6:31798482:C:G	D33H	1.000
6:31798488:A:G	S31P	1.000
6:31798493:A:G	L29P	1.000
6:31798493:A:T	L29H	1.000
6:31798499:C:A	G27V	1.000

dbSNP variants (sampled 300 via entrez): RS1000456623 (6:31806921 G>A), RS1000898675 (6:31799328 A>G), RS1000942439 (6:31807759 G>A), RS1001422238 (6:31805161 T>C), RS1001533722 (6:31801694 G>A), RS1001553206 (6:31801462 G>A,C,T), RS1001564792 (6:31801870 T>C), RS1001730562 (6:31808205 T>C), RS1002078081 (6:31804352 T>C), RS1002098092 (6:31807908 T>C,G), RS1002107846 (6:31802724 C>A), RS1002404959 (6:31807340 C>G,T), RS1002657142 (6:31798530 A>G), RS1002727805 (6:31800858 C>T), RS1003146759 (6:31798894 G>A)

Disease associations

OMIM: gene MIM:607282 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

24 associations (top):

Study	Trait	p-value
GCST004131_25	Inflammatory bowel disease	2.000000e-31
GCST004133_79	Ulcerative colitis	5.000000e-65
GCST004521_114	Autism spectrum disorder or schizophrenia	3.000000e-17
GCST004521_117	Autism spectrum disorder or schizophrenia	3.000000e-15
GCST004521_118	Autism spectrum disorder or schizophrenia	3.000000e-15
GCST004521_126	Autism spectrum disorder or schizophrenia	2.000000e-10
GCST004521_154	Autism spectrum disorder or schizophrenia	3.000000e-08
GCST004521_17	Autism spectrum disorder or schizophrenia	2.000000e-12
GCST004521_173	Autism spectrum disorder or schizophrenia	4.000000e-14
GCST004521_209	Autism spectrum disorder or schizophrenia	5.000000e-16
GCST004521_211	Autism spectrum disorder or schizophrenia	5.000000e-15
GCST004521_213	Autism spectrum disorder or schizophrenia	5.000000e-13
GCST004521_224	Autism spectrum disorder or schizophrenia	5.000000e-10
GCST004521_227	Autism spectrum disorder or schizophrenia	4.000000e-12
GCST004521_265	Autism spectrum disorder or schizophrenia	7.000000e-14
GCST004521_281	Autism spectrum disorder or schizophrenia	5.000000e-09
GCST004521_296	Autism spectrum disorder or schizophrenia	6.000000e-18
GCST004521_45	Autism spectrum disorder or schizophrenia	2.000000e-16
GCST004521_70	Autism spectrum disorder or schizophrenia	8.000000e-20
GCST004521_81	Autism spectrum disorder or schizophrenia	1.000000e-14
GCST005790_62	Rosacea symptom severity	2.000000e-11
GCST008916_30	Asthma	1.000000e-09
GCST008917_2	Asthma (childhood onset)	4.000000e-07
GCST008921_1	Asthma and major depressive disorder	2.000000e-16

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0009180	rosacea severity measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB variants

1 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs2227956	HSPA1A, HSPA1L, LSM2	3	2.25	1	carbamazepine

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
bisphenol A	increases expression, affects cotreatment, increases methylation, decreases expression	3
sodium arsenite	decreases expression, increases expression	2
Tretinoin	decreases expression	2
Cadmium Chloride	decreases expression	2
2,4,6-tribromophenol	decreases expression	1
decabromobiphenyl ether	decreases expression	1
tetrabromobisphenol A	decreases expression	1
zinc chromate	decreases expression, increases abundance	1
ochratoxin A	decreases expression	1
2,3-bis(3’-hydroxybenzyl)butyrolactone	affects cotreatment, increases expression	1
beta-methylcholine	affects expression	1
di-n-butylphosphoric acid	affects expression	1
yessotoxin	decreases expression	1
chromium hexavalent ion	decreases expression, increases abundance	1
deguelin	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	increases expression, affects cotreatment	1
pyrimidifen	increases expression	1
bisphenol B	increases expression	1
2,2’,4,4’-tetrabromodiphenyl ether	decreases expression	1
pentabrominated diphenyl ether 100	increases expression	1
hexabrominated diphenyl ether 153	decreases expression	1
jinfukang	increases expression	1
LDN 193189	affects cotreatment, increases expression	1
PP242	increases expression	1
Temozolomide	increases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Arsenic	affects methylation	1
Cisplatin	increases expression	1
Coumestrol	affects cotreatment, increases expression	1
Dichlorodiphenyl Dichloroethylene	increases expression	1

Clinical trials (associated diseases)

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