LSM4

Summary

LSM4 (LSM4 homolog, U6 small nuclear RNA and mRNA degradation associated, HGNC:17259) is a protein-coding gene on chromosome 19p13.11, encoding U6 snRNA-associated Sm-like protein LSm4 (Q9Y4Z0). 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 99.6% 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. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene.

Source: NCBI Gene 25804 — RefSeq curated summary.

At a glance

• GWAS associations: 15
• Clinical variants (ClinVar): 19 total
• Cancer dependency (DepMap): dependent in 99.6% of screened cell lines (common-essential)
• MANE Select transcript: NM_012321

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:17259
Approved symbol	LSM4
Name	LSM4 homolog, U6 small nuclear RNA and mRNA degradation associated
Location	19p13.11
Locus type	gene with protein product
Status	Approved
Aliases	YER112W
Ensembl gene	ENSG00000130520
Ensembl biotype	protein_coding
OMIM	607284
Entrez	25804

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 12 protein_coding, 2 retained_intron, 1 nonsense_mediated_decay

ENST00000252816, ENST00000593564, ENST00000593829, ENST00000594828, ENST00000597776, ENST00000600289, ENST00000881206, ENST00000881207, ENST00000922944, ENST00000922945, ENST00000922946, ENST00000950589, ENST00000950590, ENST00000950591, ENST00000950592

RefSeq mRNA: 2 — MANE Select: NM_012321 NM_001252129, NM_012321

CCDS: CCDS12374, CCDS62601

Canonical transcript exons

ENST00000593829 — 5 exons

Exon	Start	End
ENSE00001113499	18323018	18323076
ENSE00003142672	18306236	18307555
ENSE00003702217	18309678	18309861
ENSE00003705548	18316024	18316065
ENSE00003709520	18312604	18312702

Expression profiles

Bgee: expression breadth ubiquitous, 300 present calls, max score 98.46.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 98.4986 / max 466.4091, expressed in 1827 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
179993	50.0438	1820
179994	43.4697	1821
179992	4.5557	1591
179989	0.3819	143
179990	0.0307	9
179991	0.0167	7

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
mucosa of transverse colon	UBERON:0004991	98.46	gold quality
right testis	UBERON:0004534	98.20	gold quality
left testis	UBERON:0004533	98.14	gold quality
ventricular zone	UBERON:0003053	97.70	gold quality
right adrenal gland	UBERON:0001233	97.55	gold quality
right adrenal gland cortex	UBERON:0035827	97.43	gold quality
left adrenal gland cortex	UBERON:0035825	97.42	gold quality
left adrenal gland	UBERON:0001234	97.40	gold quality
embryo	UBERON:0000922	97.30	gold quality
ganglionic eminence	UBERON:0004023	97.29	gold quality
testis	UBERON:0000473	97.18	gold quality
apex of heart	UBERON:0002098	97.06	gold quality
adrenal cortex	UBERON:0001235	97.00	gold quality
right frontal lobe	UBERON:0002810	96.91	gold quality
amygdala	UBERON:0001876	96.90	gold quality
lower esophagus mucosa	UBERON:0035834	96.79	gold quality
gastrocnemius	UBERON:0001388	96.75	gold quality
nucleus accumbens	UBERON:0001882	96.72	gold quality
granulocyte	CL:0000094	96.66	gold quality
adrenal gland	UBERON:0002369	96.66	gold quality
transverse colon	UBERON:0001157	96.65	gold quality
prefrontal cortex	UBERON:0000451	96.61	gold quality
Brodmann (1909) area 9	UBERON:0013540	96.58	gold quality
cingulate cortex	UBERON:0003027	96.51	gold quality
adenohypophysis	UBERON:0002196	96.42	gold quality
anterior cingulate cortex	UBERON:0009835	96.39	gold quality
metanephros cortex	UBERON:0010533	96.35	gold quality
muscle of leg	UBERON:0001383	96.34	gold quality
hindlimb stylopod muscle	UBERON:0004252	96.33	gold quality
body of stomach	UBERON:0001161	96.24	gold quality

Single-cell (SCXA)

Detected in 7 experiment(s), a significant marker in 6.

Experiment	Marker?	Max mean expression
E-GEOD-134144	yes	30.08
E-GEOD-125970	yes	24.56
E-HCAD-10	yes	24.36
E-CURD-112	yes	11.07
E-MTAB-10553	yes	8.41
E-GEOD-76312	no	236.10
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

30 targeting LSM4, 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-6758-5P	100.00	66.21	1470
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-6499-3P	99.90	66.38	1212
HSA-MIR-4302	99.89	67.94	1187
HSA-MIR-605-3P	99.88	69.22	1833
HSA-MIR-7110-5P	99.80	67.84	1712
HSA-MIR-2052	99.79	69.37	2031
HSA-MIR-4470	99.66	69.35	1767
HSA-MIR-587	99.64	70.86	2611
HSA-MIR-6126	99.62	68.09	996
HSA-MIR-24-3P	99.59	69.97	1934
HSA-MIR-451B	99.55	68.28	1380
HSA-MIR-6733-3P	99.54	67.80	1281
HSA-MIR-122B-3P	99.21	68.90	1333
HSA-MIR-21-3P	99.21	68.95	1312
HSA-MIR-143-5P	98.98	68.87	946
HSA-MIR-4801	98.96	69.42	2096
HSA-MIR-589-5P	98.72	66.96	927
HSA-MIR-4731-3P	98.56	68.60	1860
HSA-MIR-3928-5P	98.50	67.48	980
HSA-MIR-6806-3P	98.50	67.31	980
HSA-MIR-3138	98.41	67.53	744
HSA-MIR-6801-3P	98.04	64.64	805
HSA-MIR-4303	98.01	68.13	2304
HSA-MIR-6810-3P	97.96	64.57	1023
HSA-MIR-3144-5P	97.64	65.45	646
HSA-MIR-3116	97.07	65.78	1324
HSA-MIR-1292-3P	72.98	63.40	23

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 99.6% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 9)

• LSm1-7 proteins colocalize with DCP1,DCP2 and Xrn1 in cytoplasmic foci (PMID:12515382)
• Data show that ICln159, a truncated ICln mutant, belongs to the pleckstrin homology (PH) domain family of proteins and interacts with LSm4, a protein involved in splicing and mRNA degradation. (PMID:15905169)
• Gene induces transformed phenotype when overexpressed in a cancer breast cell line. (PMID:17178857)
• LSm4 not only acts in RNA processing, but also as a co-factor in cell volume regulation. (PMID:19088440)
• C-terminal extension of Lsm4 interacts directly with the histone mRNP, contacting both SLBP and 3’hExo. (PMID:24255165)
• Results show that the RGG domain of human Lsm4 stimulates processing bodies formation. Also, a novel interaction of the Lsm4 RGG domain with HAT1 and RBBP7 was discovered, leading to the possibility of a posttranslational modifications network involved in mRNP regulation. (PMID:27247266)
• Circ_0025033 promotes the progression of ovarian cancer by activating the expression of LSM4 via targeting miR-184. (PMID:33285422)
• [Phase Separation of Purified Human LSM4 Protein]. (PMID:36976747)
• METTL3-mediated the m6A modification of SF3B4 facilitates the development of non-small cell lung cancer by enhancing LSM4 expression. (PMID:38462740)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	lsm4	ENSDARG00000023852
mus_musculus	Lsm4	ENSMUSG00000031848
rattus_norvegicus	Lsm4	ENSRNOG00000019572
drosophila_melanogaster	CG17768	FBGN0032240
caenorhabditis_elegans		WBGENE00003078

Paralogs (2): SNRPD3 (ENSG00000100028), SNRPD1 (ENSG00000167088)

Protein

Protein identifiers

U6 snRNA-associated Sm-like protein LSm4 — Q9Y4Z0 (reviewed: Q9Y4Z0)

Alternative names: Glycine-rich protein

All UniProt accessions (4): Q9Y4Z0, M0QXB0, U3KQK1, V9GZ56

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 (2): NP_001239058, NP_036453* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001163	Sm_dom_euk/arc	Domain
IPR010920	LSM_dom_sf	Homologous_superfamily
IPR027141	LSm4/Sm_D1/D3	Family
IPR034101	Lsm4	Domain
IPR047575	Sm	Domain

Pfam: PF01423

UniProt features (6 total): chain 1, domain 1, region of interest 1, compositionally biased region 1, modified residue 1, cross-link 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-Q9Y4Z0-F1	77.47	0.56

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 (2): 1, 80

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: 267 (showing top): HORIUCHI_WTAP_TARGETS_DN, GOBP_P_BODY_ASSEMBLY, GOBP_REGULATION_OF_MRNA_CATABOLIC_PROCESS, REACTOME_MRNA_DECAY_BY_5_TO_3_EXORIBONUCLEASE, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, RIZKI_TUMOR_INVASIVENESS_3D_DN, MODULE_16, PATIL_LIVER_CANCER, PUJANA_CHEK2_PCC_NETWORK, WEI_MYCN_TARGETS_WITH_E_BOX, 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

GO Biological Process (7): spliceosomal snRNP assembly (GO:0000387), mRNA splicing, via spliceosome (GO:0000398), nuclear-transcribed mRNA catabolic process (GO:0000956), RNA splicing (GO:0008380), P-body assembly (GO:0033962), RNA processing (GO:0006396), mRNA processing (GO:0006397)

GO Molecular Function (4): RNA binding (GO:0003723), U6 snRNA binding (GO:0017070), PH domain binding (GO:0042731), protein binding (GO:0005515)

GO Cellular Component (13): P-body (GO:0000932), nucleus (GO:0005634), nucleoplasm (GO:0005654), spliceosomal complex (GO:0005681), U6 snRNP (GO:0005688), cytosol (GO:0005829), membrane (GO:0016020), protein-containing complex (GO:0032991), U4/U6 x U5 tri-snRNP complex (GO:0046540), U2-type precatalytic spliceosome (GO:0071005), spliceosomal tri-snRNP complex (GO:0097526), Lsm2-8 complex (GO:0120115), 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
spliceosomal snRNP complex	2
mRNA splicing, via spliceosome	1
protein-RNA complex assembly	1
RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	1
mRNA processing	1
mRNA catabolic process	1
membraneless organelle assembly	1
gene expression	1
RNA biosynthetic process	1
primary metabolic process	1
mRNA metabolic process	1
nucleic acid binding	1
snRNA binding	1
protein domain specific binding	1
binding	1
cytoplasmic ribonucleoprotein granule	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
nuclear protein-containing complex	1
ribonucleoprotein complex	1
Lsm2-8 complex	1
cytoplasm	1
cellular_component	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
Sm-like protein family complex	1
protein-containing complex	1

Protein interactions and networks

STRING

2538 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LSM4	LSM3	P62310	998
LSM4	LSM6	P62312	994
LSM4	LSM8	O95777	993
LSM4	LSM7	Q9UK45	988
LSM4	LSM1	O15116	988
LSM4	LSM5	Q9Y4Y9	987
LSM4	XRN1	Q8IZH2	940
LSM4	LSM2	Q9Y333	902
LSM4	EDC3	Q96F86	882
LSM4	SNRPD2	P43330	860
LSM4	DCP1A	Q9NPI6	772
LSM4	DCP2	Q8IU60	727
LSM4	EDC4	Q6P2E9	696
LSM4	TIA1	P31483	686
LSM4	TIAL1	Q01085	630

IntAct

138 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
LSM7	LSM4	psi-mi:“MI:0915”(physical association)	0.890
LSM4	LSM7	psi-mi:“MI:0915”(physical association)	0.890
LSM1	LSM4	psi-mi:“MI:0915”(physical association)	0.840
LSM1	LSM6	psi-mi:“MI:0914”(association)	0.840
LSM6	LSM1	psi-mi:“MI:0914”(association)	0.840
LSM2	LSM8	psi-mi:“MI:0915”(physical association)	0.790
CALCOCO2	LSM4	psi-mi:“MI:0915”(physical association)	0.780
LSM4	CALCOCO2	psi-mi:“MI:0915”(physical association)	0.780
PATL1	LSM1	psi-mi:“MI:0914”(association)	0.770
SART3	PRPF4	psi-mi:“MI:0914”(association)	0.730
PRPF3	PRPF4	psi-mi:“MI:0914”(association)	0.730
LSM4	PSTPIP1	psi-mi:“MI:0915”(physical association)	0.720
PSTPIP1	LSM4	psi-mi:“MI:0915”(physical association)	0.720

BioGRID (282): LSM4 (Two-hybrid), LSM4 (Two-hybrid), LSM4 (Two-hybrid), ZBTB10 (Two-hybrid), L3MBTL3 (Two-hybrid), LSM4 (Two-hybrid), HNRNPR (Co-fractionation), KLC2 (Co-fractionation), LRPPRC (Co-fractionation), LSM1 (Co-fractionation), LSM2 (Co-fractionation), LSM3 (Co-fractionation), LSM4 (Co-fractionation), LSM4 (Co-fractionation), LSM6 (Co-fractionation)

ESM2 similar proteins: B0RTY9, B0U1E7, B2FL26, B2I691, B4SRA5, F4K4E3, O42661, O44437, O88984, P58797, P62314, P62315, P62318, P62320, P62323, Q0VME7, Q10013, Q15691, Q17348, Q19952, Q1RMS5, Q1ZXK3, Q2P1M4, Q3BUR4, Q3ZBD9, Q3ZBK6, Q3ZC10, Q43582, Q4R5F6, Q5GYM1, Q5R752, Q5ZLC7, Q61166, Q66HR2, Q66T82, Q6P848, Q6V291, Q87F71, Q8PLQ4, Q99JX7

Diamond homologs: F4K4E3, O14352, O59734, P40070, Q19952, Q3ZBK6, Q43582, Q54KX4, Q54TF6, Q9LGE6, Q9LM92, Q9QXA5, Q9S7E6, Q9UUC6, Q9Y4Z0, Q9ZRU9, O35900, O44437, P43321, P62306, P62307, P62321, Q17348, Q24297, Q3T0Z8, Q552U1, Q55EX5, Q8QZX5, Q969L4, Q9SUM2, Q9Y333, P62314, P62315, P62318, P62320, P62323, Q3ZC10, Q4R5F6, Q9VU02, A5DRQ6

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
LSM4	“form complex”	“U4/U6.U5 snRNP complex”	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 100 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	65.8×	2e-10
Metabolism of non-coding RNA	5	39.2×	5e-06
mRNA Splicing	20	27.1×	7e-22
Processing of Capped Intron-Containing Pre-mRNA	24	24.3×	4e-25
mRNA Splicing - Major Pathway	31	20.9×	6e-31
snRNP Assembly	7	18.3×	4e-06
mRNA Polyadenylation	16	17.4×	4e-14
mRNA Splicing - Minor Pathway	6	16.6×	5e-05

GO biological processes:

GO term	Partners	Fold	FDR
spliceosomal snRNP assembly	10	61.2×	4e-14
spliceosomal tri-snRNP complex assembly	5	59.1×	9e-07
U2-type prespliceosome assembly	8	52.6×	2e-10
RNA splicing, via transesterification reactions	7	46.0×	1e-08
spliceosomal complex assembly	6	38.0×	7e-07
mRNA splicing, via spliceosome	32	30.9×	5e-37
RNA splicing	18	16.7×	5e-15
mRNA processing	18	14.9×	3e-14

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	11
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

604 predictions. Top by Δscore:

Variant	Effect	Δscore
19:18309857:CCGTC:C	acceptor_gain	1.0000
19:18309858:CGTC:C	acceptor_gain	1.0000
19:18309858:CGTCC:C	acceptor_gain	1.0000
19:18309859:GTC:G	acceptor_gain	1.0000
19:18309860:TC:T	acceptor_gain	1.0000
19:18309861:CC:C	acceptor_gain	1.0000
19:18309862:C:CC	acceptor_gain	1.0000
19:18309862:C:T	acceptor_gain	1.0000
19:18312602:A:AC	donor_gain	1.0000
19:18312602:AC:A	donor_gain	1.0000
19:18312603:C:CC	donor_gain	1.0000
19:18312603:CC:C	donor_gain	1.0000
19:18312623:T:TA	donor_gain	1.0000
19:18312698:ACCAA:A	acceptor_gain	1.0000
19:18312699:CCAA:C	acceptor_gain	1.0000
19:18312699:CCAAC:C	acceptor_gain	1.0000
19:18312700:CAA:C	acceptor_gain	1.0000
19:18312700:CAAC:C	acceptor_gain	1.0000
19:18312701:AA:A	acceptor_gain	1.0000
19:18312701:AACT:A	acceptor_loss	1.0000
19:18312702:AC:A	acceptor_loss	1.0000
19:18312703:C:CC	acceptor_gain	1.0000
19:18312703:CTAG:C	acceptor_loss	1.0000
19:18323053:T:TA	donor_gain	1.0000
19:18306537:CAG:C	acceptor_gain	0.9900
19:18309865:C:CT	acceptor_gain	0.9900
19:18309866:G:T	acceptor_gain	0.9900
19:18312599:CCCA:C	donor_loss	0.9900
19:18312600:CCA:C	donor_loss	0.9900
19:18312603:C:CT	donor_loss	0.9900

AlphaMissense

900 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:18309800:A:G	L69P	1.000
19:18309805:C:A	K67N	1.000
19:18309805:C:G	K67N	1.000
19:18309807:T:C	K67E	1.000
19:18309809:A:T	I66N	1.000
19:18309818:C:A	G63V	1.000
19:18309818:C:T	G63D	1.000
19:18309819:C:A	G63C	1.000
19:18309819:C:G	G63R	1.000
19:18309819:C:T	G63S	1.000
19:18309822:G:T	R62S	1.000
19:18309824:A:C	I61S	1.000
19:18309824:A:T	I61N	1.000
19:18309829:G:C	C59W	1.000
19:18309831:A:G	C59R	1.000
19:18309847:G:C	F53L	1.000
19:18309847:G:T	F53L	1.000
19:18309848:A:C	F53C	1.000
19:18309848:A:G	F53S	1.000
19:18309849:A:G	F53L	1.000
19:18309857:C:A	G50V	1.000
19:18309857:C:T	G50E	1.000
19:18309858:C:A	G50W	1.000
19:18312620:A:T	V43D	1.000
19:18312621:C:A	V43F	1.000
19:18312629:A:G	L40P	1.000
19:18312637:G:C	N37K	1.000
19:18312637:G:T	N37K	1.000
19:18312638:T:A	N37I	1.000
19:18312640:C:A	M36I	1.000

dbSNP variants (sampled 300 via entrez): RS1000029179 (19:18308693 G>A,C), RS1000201773 (19:18306632 A>C,G), RS1000260355 (19:18324369 T>C), RS1000365262 (19:18315878 G>A), RS1000378967 (19:18317970 G>A,T), RS1000597842 (19:18323065 G>A,C), RS1001163829 (19:18317605 T>C), RS1001168986 (19:18316267 A>G), RS1001319571 (19:18311823 C>G), RS1001387320 (19:18322270 T>C), RS1001724148 (19:18323472 T>G), RS1001923011 (19:18307121 C>G,T), RS1002102279 (19:18315965 C>A,G,T), RS1002111625 (19:18322816 A>T), RS1002176437 (19:18323820 G>A,C)

Disease associations

OMIM: gene MIM:607284 | 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
GCST004601_188	Red blood cell count	9.000000e-10
GCST004602_268	Mean corpuscular volume	4.000000e-13
GCST004630_61	Mean corpuscular hemoglobin	1.000000e-10
GCST005580_104	Intraocular pressure	5.000000e-08
GCST007344_72	Estimated glomerular filtration rate	4.000000e-08
GCST007576_93	Chronotype	4.000000e-11
GCST008832_10	Gastroesophageal reflux disease	2.000000e-10
GCST90002390_533	Mean corpuscular hemoglobin	2.000000e-20
GCST90002392_87	Mean corpuscular volume	1.000000e-24
GCST90002393_653	Monocyte count	1.000000e-16
GCST90002396_28	Mean reticulocyte volume	1.000000e-13
GCST90002397_197	Mean spheric corpuscular volume	8.000000e-21
GCST90002401_261	Platelet distribution width	7.000000e-18
GCST90002403_283	Red blood cell count	8.000000e-25
GCST90002405_542	Reticulocyte count	1.000000e-09

EFO canonical traits (8, from GWAS)

EFO ID	Trait name
EFO:0004305	erythrocyte count
EFO:0004527	mean corpuscular hemoglobin
EFO:0004695	intraocular pressure measurement
EFO:0008328	chronotype measurement
EFO:0005091	monocyte count
EFO:0010701	mean reticulocyte volume
EFO:0007984	platelet component distribution width
EFO:0007986	reticulocyte count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
bisphenol A	affects expression, decreases expression, increases expression	3
sodium arsenite	decreases expression, affects cotreatment, increases abundance, increases expression	3
Arsenic	affects methylation, affects cotreatment, decreases expression, increases abundance	2
bisphenol F	increases expression	1
arsenite	affects binding, increases reaction	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
cobaltous chloride	decreases expression	1
manganese chloride	affects cotreatment, decreases expression, increases abundance	1
di-n-butylphosphoric acid	affects expression	1
2-palmitoylglycerol	increases expression	1
K 7174	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
erucylphospho-N,N,N-trimethylpropylammonium	decreases expression	1
bisphenol B	increases expression	1
LDN 193189	increases expression, affects cotreatment	1
(+)-JQ1 compound	decreases expression	1
Bortezomib	decreases expression	1
Resveratrol	increases expression	1
Temozolomide	increases expression	1
Vorinostat	increases expression	1
Benzo(a)pyrene	affects methylation	1
Coumestrol	increases expression	1
Diazinon	increases methylation	1
Doxorubicin	increases expression	1
Ivermectin	decreases expression	1
Manganese	affects cotreatment, decreases expression, increases abundance	1
Ozone	increases expression, increases abundance	1
Phenobarbital	affects expression	1
Quercetin	increases expression	1
Ribonucleotides	affects binding	1

Clinical trials (associated diseases)

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