LSM10

Summary

LSM10 (LSM10, U7 small nuclear RNA associated, HGNC:17562) is a protein-coding gene on chromosome 1p34.3, encoding U7 snRNA-associated Sm-like protein LSm10 (Q969L4). Appears to function in the U7 snRNP complex that is involved in histone 3’-end processing. It is a selective cancer dependency (DepMap: 32.3% of cell lines).

Enables U7 snRNA binding activity. Involved in positive regulation of G1/S transition of mitotic cell cycle. Located in Cajal body. Part of U7 snRNP.

Source: NCBI Gene 84967 — automated summary from GO annotations (Alliance of Genome Resources).

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 20 total
• GTEx eGene: eQTL in 27 tissues, sQTL in 12 (q < 0.05)
• Cancer dependency (DepMap): dependent in 32.3% of screened cell lines
• Constraint (gnomAD): pLI 0.00 (LoF-tolerant), LOEUF 1.59 (unconstrained)
• MANE Select transcript: NM_032881

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:17562
Approved symbol	LSM10
Name	LSM10, U7 small nuclear RNA associated
Location	1p34.3
Locus type	gene with protein product
Status	Approved
Aliases	MGC15749
Ensembl gene	ENSG00000181817
Ensembl biotype	protein_coding
OMIM	617909
Entrez	84967

Gene structure

Transcript identifiers

Ensembl transcripts: 20 — 17 protein_coding, 2 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

MANE Select: ENST00000315732

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 1, TSL 3: 2

ENST00000315732, ENST00000476041, ENST00000489912, ENST00000861455, ENST00000861456, ENST00000861457, ENST00000861458, ENST00000861459, ENST00000861460, ENST00000861461, ENST00000861462, ENST00000861463, ENST00000861464, ENST00000916574, ENST00000916575, ENST00000916576, ENST00000916577, ENST00000967723, ENST00001039961, ENST00001144290

RefSeq mRNA: 1 — MANE Select: NM_032881 NM_032881

CCDS: CCDS408

Canonical transcript exons

ENST00000315732 — 2 exons

Exon	Start	End
ENSE00001274385	36397767	36397908
ENSE00001274393	36393436	36394153

Expression profiles

Bgee: expression breadth ubiquitous, 245 present calls, max score 97.36.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 32.2106 / max 190.5982, expressed in 1819 samples.

Highest expression (Bgee): hindlimb stylopod muscle, gastrocnemius, granulocyte, muscle of leg, apex of heart.

Genetic regulation across tissues (GTEx eQTL / sQTL)

LSM10 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 27 tissues and its splicing (sQTL) in 12 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

showing 20 of 39 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Artery Tibial	sqtl	8.9e-22	+0.72	1:36358720:C:T
Nerve Tibial	sqtl	6.5e-21	+0.65	1:36358720:C:T
Adipose Subcutaneous	sqtl	1.1e-17	+0.61	1:36358720:C:T
Brain Cortex	eqtl	6.1e-15	+0.85	1:36393562:T:C
Muscle Skeletal	eqtl	2.6e-14	-0.34	1:36397922:A:G
Esophagus Muscularis	sqtl	1.1e-10	+1.28	1:36362569:T:G
Brain Cerebellum	eqtl	9.0e-09	+0.84	1:36393562:T:C
Colon Sigmoid	sqtl	1.0e-07	+1.31	1:36362569:T:G
Breast Mammary Tissue	sqtl	1.9e-07	+0.48	1:36358720:C:T
Brain Cerebellar Hemisphere	eqtl	3.1e-07	+0.63	1:36393562:T:C
Testis	eqtl	3.2e-07	-0.13	1:36396392:A:G
Brain Anterior cingulate cortex BA24	eqtl	4.9e-07	+0.64	1:36393562:T:C
Brain Frontal Cortex BA9	eqtl	2.0e-05	+0.61	1:36393562:T:C
Skin Sun Exposed Lower leg	eqtl	1.2e-04	+0.12	1:36393316:C:T
Thyroid	sqtl	1.2e-04	+0.80	1:36362569:T:G
Brain Putamen basal ganglia	eqtl	1.9e-04	+0.55	1:36393562:T:C
Stomach	sqtl	3.4e-04	+1.04	1:36362569:T:G
Artery Tibial	eqtl	4.3e-04	+0.09	1:36393316:C:T
Brain Hippocampus	eqtl	4.9e-04	+0.45	1:36393562:T:C
Cells Cultured fibroblasts	eqtl	1.2e-03	+0.07	1:36399960:G:A

FANTOM5 promoters

1 alternative TSS:

Promoter ID	TPM avg	Samples expressed
11726	32.2106	1819

Top tissues by expression

showing 100 of 253 tissues by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
hindlimb stylopod muscle	UBERON:0004252	97.36	gold quality
gastrocnemius	UBERON:0001388	96.95	gold quality
granulocyte	CL:0000094	96.42	gold quality
muscle of leg	UBERON:0001383	96.26	gold quality
apex of heart	UBERON:0002098	95.95	gold quality
leukocyte	CL:0000738	95.63	gold quality
monocyte	CL:0000576	95.55	gold quality
right atrium auricular region	UBERON:0006631	94.66	gold quality
skeletal muscle tissue	UBERON:0001134	94.57	gold quality
tibialis anterior	UBERON:0001385	94.52	gold quality
quadriceps femoris	UBERON:0001377	94.49	gold quality
muscle layer of sigmoid colon	UBERON:0035805	94.27	gold quality
deltoid	UBERON:0001476	94.23	gold quality
vastus lateralis	UBERON:0001379	94.15	gold quality
lower esophagus muscularis layer	UBERON:0035833	94.15	gold quality
lower esophagus	UBERON:0013473	94.12	gold quality
heart left ventricle	UBERON:0002084	93.95	gold quality
cardiac atrium	UBERON:0002081	93.90	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	93.86	gold quality
cardiac ventricle	UBERON:0002082	93.78	gold quality
prefrontal cortex	UBERON:0000451	93.44	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	93.44	gold quality
biceps brachii	UBERON:0001507	93.21	gold quality
muscle tissue	UBERON:0002385	93.20	gold quality
anterior cingulate cortex	UBERON:0009835	93.11	gold quality
lymph node	UBERON:0000029	93.07	gold quality
mucosa of stomach	UBERON:0001199	93.00	gold quality
spleen	UBERON:0002106	92.83	gold quality
heart	UBERON:0000948	92.70	gold quality
adenohypophysis	UBERON:0002196	92.64	gold quality
hypothalamus	UBERON:0001898	92.63	gold quality
blood	UBERON:0000178	92.42	gold quality
putamen	UBERON:0001874	92.35	gold quality
Brodmann (1909) area 9	UBERON:0013540	92.32	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	92.30	gold quality
left uterine tube	UBERON:0001303	92.17	gold quality
caudate nucleus	UBERON:0001873	92.17	gold quality
right frontal lobe	UBERON:0002810	92.15	gold quality
left coronary artery	UBERON:0001626	92.12	gold quality
stromal cell of endometrium	CL:0002255	92.10	gold quality
nucleus accumbens	UBERON:0001882	92.09	gold quality
right coronary artery	UBERON:0001625	92.03	gold quality
amygdala	UBERON:0001876	91.90	gold quality
vermiform appendix	UBERON:0001154	91.87	gold quality
coronary artery	UBERON:0001621	91.57	gold quality
ascending aorta	UBERON:0001496	91.41	gold quality
mucosa of transverse colon	UBERON:0004991	91.41	gold quality
thoracic aorta	UBERON:0001515	91.40	gold quality
pituitary gland	UBERON:0000007	91.29	gold quality
right lobe of liver	UBERON:0001114	91.18	gold quality
omental fat pad	UBERON:0010414	91.14	gold quality
peritoneum	UBERON:0002358	91.11	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	90.97	gold quality
aorta	UBERON:0000947	90.94	gold quality
body of stomach	UBERON:0001161	90.86	gold quality
smooth muscle tissue	UBERON:0001135	90.83	gold quality
descending thoracic aorta	UBERON:0002345	90.81	gold quality
popliteal artery	UBERON:0002250	90.73	gold quality
tibial artery	UBERON:0007610	90.71	gold quality
islet of Langerhans	UBERON:0000006	90.67	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	90.49	gold quality
neocortex	UBERON:0001950	90.46	gold quality
adipose tissue of abdominal region	UBERON:0007808	90.44	gold quality
frontal cortex	UBERON:0001870	90.42	gold quality
body of uterus	UBERON:0009853	90.39	gold quality
esophagus	UBERON:0001043	90.19	gold quality
endocervix	UBERON:0000458	90.02	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	90.01	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	89.98	gold quality
heart right ventricle	UBERON:0002080	89.97	gold quality
left adrenal gland cortex	UBERON:0035825	89.88	gold quality
small intestine Peyer’s patch	UBERON:0003454	89.85	gold quality
adult mammalian kidney	UBERON:0000082	89.70	gold quality
right lobe of thyroid gland	UBERON:0001119	89.68	gold quality
left adrenal gland	UBERON:0001234	89.64	gold quality
transverse colon	UBERON:0001157	89.63	gold quality
gall bladder	UBERON:0002110	89.61	gold quality
substantia nigra	UBERON:0002038	89.53	gold quality
forebrain	UBERON:0001890	89.51	gold quality
caecum	UBERON:0001153	89.45	gold quality
right ovary	UBERON:0002118	89.45	gold quality
left lobe of thyroid gland	UBERON:0001120	89.30	gold quality
right adrenal gland	UBERON:0001233	89.29	gold quality
metanephros cortex	UBERON:0010533	89.27	gold quality
spinal cord	UBERON:0002240	89.22	gold quality
right adrenal gland cortex	UBERON:0035827	89.22	gold quality
ectocervix	UBERON:0012249	89.14	gold quality
colon	UBERON:0001155	89.13	gold quality
lower esophagus mucosa	UBERON:0035834	89.09	gold quality
cerebral cortex	UBERON:0000956	89.01	gold quality
left ovary	UBERON:0002119	88.98	gold quality
adrenal cortex	UBERON:0001235	88.91	gold quality
upper lobe of left lung	UBERON:0008952	88.90	gold quality
brain	UBERON:0000955	88.85	gold quality
body of tongue	UBERON:0011876	88.85	gold quality
large intestine	UBERON:0000059	88.78	gold quality
minor salivary gland	UBERON:0001830	88.74	gold quality
fundus of stomach	UBERON:0001160	88.46	gold quality
tibial nerve	UBERON:0001323	88.43	gold quality
small intestine	UBERON:0002108	88.43	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	12.85

HPA expression

RNA tissue specificity: Low tissue specificity

showing 60 of 76 HPA tissues / cells by nTPM:

Tissue / cell	Axis	nTPM
Skeletal muscle	tissue	151.5
Tongue	tissue	102.8
Lymph node	tissue	48.9
Tonsil	tissue	44.5
Heart muscle	tissue	43.3
Pituitary gland	tissue	39.6
Parathyroid gland	tissue	34.7
Spleen	tissue	32.3
Locus coeruleus	tissue	30.2
Appendix	tissue	30.2
Choroid plexus	tissue	29.2
Urinary bladder	tissue	29.0
Pancreas	tissue	28.8
Seminal vesicle	tissue	28.7
Epididymis	tissue	28.7
Salivary gland	tissue	27.4
Vagina	tissue	26.9
Liver	tissue	26.5
Nucleus accumbens	tissue	26.3
Smooth muscle	tissue	26.1
Postcentral gyrus	tissue	25.9
Ovary	tissue	25.5
Thymus	tissue	25.3
Hippocampus	tissue	25.2
Adipose tissue	tissue	23.6
Bone marrow	tissue	22.5
Kidney	tissue	21.4
Gallbladder	tissue	21.3
Thyroid gland	tissue	20.8
Colon	tissue	20.2
Prostate	tissue	19.5
Stomach 1	tissue	19.1
Duodenum	tissue	18.9
Lung	tissue	18.7
Breast	tissue	18.6
Cervix	tissue	18.1
Adrenal gland	tissue	17.8
Esophagus	tissue	17.4
Caudate putamen	tissue	17.2
Fallopian tube	tissue	17.1
Placenta	tissue	16.9
Rectum	tissue	16.6
Small intestine	tissue	16.5
Testis	tissue	16.2
Frontal cortex	tissue	15.7
Endometrium 1	tissue	14.6
Skin 1	tissue	14.0
Hippocampal formation	tissue	10.0
Superior colliculi	tissue	9.7
Pons	tissue	9.5
Spinal cord	tissue	9.5
Medulla oblongata	tissue	9.4
Thalamus	tissue	9.4
Cerebral cortex	tissue	9.3
Somatosensory cortex	tissue	9.3
Retina	tissue	9.0
Periaqueductal gray	tissue	8.4
Substantia nigra	tissue	8.3
Midbrain	tissue	8.2
Hypothalamus	tissue	8.1

Brain sub-regions (HPA Brain Atlas): detected in 189; highest nTPM — Blood vessel (37.1), Arcuate nucleus (36.8), Ventromedial nucleus (34.6), Posterior thalamic nucleus (33.4), Lateral hypothalamic area (32.0).

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

Targeting LSM10 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

22 miRNAs:

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-4455	100.00	65.48	1587
HSA-MIR-4525	99.94	64.38	675
HSA-MIR-5010-5P	99.94	64.11	705
HSA-MIR-3714	99.71	70.74	2671
HSA-MIR-4663	99.62	65.33	957
HSA-MIR-4756-3P	99.62	66.30	1319
HSA-MIR-24-3P	99.59	69.97	1934
HSA-MIR-4753-5P	99.54	68.51	1356
HSA-MIR-6731-5P	99.28	67.42	2375
HSA-MIR-8085	99.28	67.56	2362
HSA-MIR-5100	99.11	67.52	1098
HSA-MIR-219A-1-3P	98.91	67.87	639
HSA-MIR-1288-5P	98.85	67.01	734
HSA-MIR-3922-5P	98.77	66.53	1059
HSA-MIR-1227-5P	98.65	65.32	1549
HSA-MIR-9903	98.47	66.70	748
HSA-MIR-4717-5P	98.19	67.97	894
HSA-MIR-6730-5P	98.03	68.12	1299
HSA-MIR-5681A	97.99	67.17	1658
HSA-MIR-146B-3P	97.83	65.29	782
HSA-MIR-7154-3P	97.65	65.02	985
HSA-MIR-3192-5P	96.98	65.76	1926

Functional genomics

gnomAD constraint: pLI 0.00409, LOEUF 1.59, missense Z 0.806 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD RMC): no regional variation along ENST00000315732 — one region, missense o/e 0.87. DepMap (CRISPR cell-line fitness): dependent in 32.3% of screened cell lines.

Most-dependent cell lines (DepMap gene-effect, lower = stronger; ≤ −0.5 shown): SU-DHL-8 (-1.542), PA-TU-8988T (-1.515), TYK-nu (-1.385), KP-4 (-1.376), SF126 (-1.224), ChaGo-K-1 (-1.183), ARH-77 (-1.182), EW-7 (-1.164), CAL 27 (-1.161), SJSA-1 (-1.125), COR-L105 (-1.121), Panc 03.27 (-1.09), Hey (-1.087), JHU-011 (-1.037), SEM (-0.997).

Literature-anchored findings (GeneRIF, showing 6)

• Purified U7 snRNPs lack the Sm proteins D1 and D2 but contain Lsm10, a new 14 kDa Sm D1-like protein. (PMID:11574479)
• Lsm10 and Lsm11, which replace the Sm proteins D1 and D2 in the histone RNA processing U7 snRNPs, associate with pICln in vitro and in vivo without receiving sDMA modifications and with PRMT5 and SMN complexes (PMID:16087681)
• The overexpression of Lsm10 and Lsm11 increases the cellular levels of U7 snRNP but has no effect on histone pre-mRNA processing. (PMID:16914750)
• The subnuclear organization of histone gene regulatory proteins and 3’ end processing factors (NPAT/LSM10) of normal somatic and embryonic stem cells is compromised in selected human cancer cell types. (PMID:19277982)
• FLASH plays two roles in 3’ end processing of histone pre-mRNAs: It interacts with Lsm11 to form a docking platform for the polyadenylation factors, and it cooperates with SLBP to recruit U7 snRNP to histone pre-mRNA. (PMID:28289156)
• While the molecular basis for this altered cleavage activity is unknown, one possibility is that binding of Lsm10 and Lsm11 to the spliceosomal Sm site affects the overall geometry of the U7-specific Sm ring, resulting in misalignment of the CPSF73 endonuclease with the substrate. (PMID:31819999)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	lsm10	ENSDARG00000101222
		ENSDARG00000109563
mus_musculus	Lsm10	ENSMUSG00000050188
drosophila_melanogaster	Lsm10	FBGN0033554
caenorhabditis_elegans	K07A1.15	WBGENE00010619

Additional cross-species homologs

Sequence homologs in species beyond Ensembl Compara’s model organisms, by Diamond local protein alignment (% sequence identity; best hit per species). Lower-identity rows are more distant homologs. The matched accessions’ gene symbols aren’t in biobtree yet, so each row shows the UniProt accession.

Organism	UniProt	Identity	Method
Bos taurus	Q3ZC10	100.0%	Diamond
Macaca fascicularis	Q4R5F6	100.0%	Diamond
Arabidopsis thaliana	Q9SY09	92.7%	Diamond
Dictyostelium discoideum	Q54TF6	70.2%	Diamond
Schizosaccharomyces pombe 972h-	O14352	69.6%	Diamond

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

Symbol	Type	Entrez
SNORA63C	snoRNA	109616970
OSCP1	protein-coding	127700
MRPS15	protein-coding	64960
EVA1B	protein-coding	55194
MNMIP1	protein-coding	79729
STK40	protein-coding	83931
THRAP3	protein-coding	9967
CSF3R	protein-coding	1441

Protein

Protein identifiers

U7 snRNA-associated Sm-like protein LSm10 — Q969L4 (reviewed: Q969L4)

All UniProt accessions (1): Q969L4

UniProt curated annotations — full annotation on UniProt →

Function. Appears to function in the U7 snRNP complex that is involved in histone 3’-end processing. Increases U7 snRNA levels but not histone 3’-end pre-mRNA processing activity, when overexpressed. Required for cell cycle progression from G1 to S phases. Binds specifically to U7 snRNA. Binds to the downstream cleavage product (DCP) of histone pre-mRNA in a U7 snRNP dependent manner.

Subunit / interactions. Component of the heptameric ring U7 snRNP complex, or U7 Sm protein core complex, at least composed of LSM10, LSM11, SNRPB, SNRPD3, SNRPE, SNRPF, SNRPG and U7 snRNA. Formation of the U7 snRNP is an ATP-dependent process mediated by a specialized SMN complex containing at least the Sm protein core complex and additionally, the U7-specific LSM10 and LSM11 proteins. Interacts with CLNS1A and SMN.

Subcellular location. Nucleus.

Post-translational modifications. Not methylated. Methylation is not necessary for interaction with SMN.

Similarity. Belongs to the snRNP Sm proteins family.

RefSeq proteins (1): NP_116270* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001163	Sm_dom_euk/arc	Domain
IPR010920	LSM_dom_sf	Homologous_superfamily
IPR047575	Sm	Domain
IPR052840	U7_snRNA_Sm-like	Family

Pfam: PF01423

UniProt features (14 total): strand 8, helix 3, chain 1, domain 1, turn 1

Structure

Experimental structures (PDB)

5 structures by resolution:

PDB	Title	Method	Resolution (Å)
9NH5	CRYO-EM STRUCTURE OF HUMAN U7 SNRNP WITH METHYLATED noncleavable H2A* SUBSTRATE PRE-MRNA …	ELECTRON MICROSCOPY	2.82
9NH6	CRYO-EM STRUCTURE OF HUMAN U7 SNRNP WITH METHYLATED noncleavable H2A* SUBSTRATE PRE-MRNA …	ELECTRON MICROSCOPY	2.82
9N96	CRYO-EM STRUCTURE OF human U7 SM RING IN COMPLEX WITH SYMPLEKIN N-TERMINAL DOMAIN	ELECTRON MICROSCOPY	3.18
6V4X	Cryo-EM structure of an active human histone pre-mRNA 3’-end processing machinery at 3.2 …	ELECTRON MICROSCOPY	3.2
9NB1	CRYO-EM STRUCTURE OF human U7 SNRNP WITH MUTANT LSM11 that disrupts contacts with CPSF73	ELECTRON MICROSCOPY	3.85

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q969L4-F1	88.30	0.73

Human Protein Atlas

Protein class: Predicted intracellular proteins, Essential proteins

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): nucleoplasm; nuclear bodies

Antibody reliability (HPA): IF supported

Function

Pathways and Gene Ontology

Reactome pathways

3 curated (TAS) of 7; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

7 pathways:

ID	Pathway	Evidence
R-HSA-73856	RNA Polymerase II Transcription Termination	curated
R-HSA-77588	SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs	curated
R-HSA-111367	SLBP independent Processing of Histone Pre-mRNAs	curated
R-HSA-74160	Gene expression (Transcription)	—
R-HSA-8953854	Metabolism of RNA	—
R-HSA-75067	Processing of Capped Intronless Pre-mRNA	—
R-HSA-73857	RNA Polymerase II Transcription	—

MSigDB gene sets: 139 (showing top): GOBP_CELL_CYCLE_PHASE_TRANSITION, GOBP_POSITIVE_REGULATION_OF_MITOTIC_CELL_CYCLE, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GOBP_RNA_METHYLATION, GOBP_POSITIVE_REGULATION_OF_G1_S_TRANSITION_OF_MITOTIC_CELL_CYCLE, WEI_MYCN_TARGETS_WITH_E_BOX, GOBP_RNA_MODIFICATION, GOBP_REGULATION_OF_CELL_CYCLE, GOBP_MRNA_3_END_PROCESSING, GOBP_REGULATION_OF_CELL_CYCLE_G1_S_PHASE_TRANSITION, chr1p34, GOBP_POSITIVE_REGULATION_OF_CELL_CYCLE_PROCESS, GOBP_CELL_CYCLE_G1_S_PHASE_TRANSITION, GOBP_RNA_CAPPING, GOBP_RNA_SPLICING

GO Biological Process (6): mRNA 3’-end processing by stem-loop binding and cleavage (GO:0006398), RNA splicing (GO:0008380), 7-methylguanosine cap hypermethylation (GO:0036261), nuclear histone mRNA catabolic process (GO:0071045), positive regulation of G1/S transition of mitotic cell cycle (GO:1900087), mRNA processing (GO:0006397)

GO Molecular Function (4): histone pre-mRNA DCP binding (GO:0071208), U7 snRNA binding (GO:0071209), RNA binding (GO:0003723), protein binding (GO:0005515)

GO Cellular Component (7): nucleoplasm (GO:0005654), U7 snRNP (GO:0005683), Cajal body (GO:0015030), nuclear body (GO:0016604), cytoplasmic U snRNP body (GO:0071254), nucleus (GO:0005634), ribonucleoprotein complex (GO:1990904)

Reactome top-level categories

4 top-level categories:

Category	Pathways
Processing of Capped Intronless Pre-mRNA	2
RNA Polymerase II Transcription	1
Gene expression (Transcription)	1
Metabolism of RNA	1

GO top-level categories

24 GO namespaces:

Category	Terms
RNA processing	2
histone mRNA metabolic process	1
mRNA 3’-end processing	1
RNA methylation	1
RNA capping	1
histone mRNA catabolic process	1
G1/S transition of mitotic cell cycle	1
positive regulation of mitotic cell cycle phase transition	1
positive regulation of cell cycle G1/S phase transition	1
regulation of G1/S transition of mitotic cell cycle	1
mRNA metabolic process	1
RNA binding	1
snRNA binding	1
nucleic acid binding	1
binding	1
nuclear lumen	1
cellular anatomical structure	1
small nuclear ribonucleoprotein complex	1
nuclear ribonucleoprotein granule	1
nucleoplasm	1
intracellular membraneless organelle	1
cytoplasmic ribonucleoprotein granule	1
intracellular membrane-bounded organelle	1
protein-containing complex	1

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 6 of 17 annotations. The rest are phylogenetic / computational / electronic (IEA).

6 experimentally-supported GO terms:

GO term	NS	Evidence
positive regulation of G1/S transition of mitotic cell cycle	BP	mutant phenotype
Cajal body	CC	direct assay
U7 snRNP	CC	direct assay
nuclear body	CC	direct assay
nucleoplasm	CC	direct assay
U7 snRNA binding	MF	physical interaction

Protein interactions and networks

STRING

showing 15 of 1,061 interactions by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LSM10	LSM11	P83369	921
LSM10	SNRPD1	P13641	812
LSM10	SNRPD2	P43330	774
LSM10	SLBP	Q14493	772
LSM10	CPSF3	Q9UKF6	748
LSM10	SYMPK	Q92797	743
LSM10	SNRPD3	P43331	709
LSM10	SNRPE	P08578	697
LSM10	NPAT	Q14207	691
LSM10	CPSF2	Q9P2I0	686
LSM10	LSM8	O95777	642
LSM10	LSM2	Q9Y333	633
LSM10	LSM6	P62312	628
LSM10	LSM12	Q3MHD2	627
LSM10	LSM4	Q9Y4Z0	615

IntAct

Human interaction partners of LSM10 in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

2 partners by confidence:

Partner	Interaction type	MIscore	Records
LSM3	physical association	0.780	4
CASP4	physical association	0.000	1

BioGRID (34 interactions; top human partners by supporting records): LSM3 (Two-hybrid; 4 records), CLNS1A (Reconstituted Complex; 2 records), LSM6 (Affinity Capture-MS; 2 records), SMN1 (Reconstituted Complex; 2 records), SNRPF (Affinity Capture-MS; 2 records), SNRPG (Affinity Capture-MS; 2 records), C16orf72 (Negative Genetic), KRAS (Negative Genetic), MIR10B (Protein-RNA), MIR128-1 (Protein-RNA), MIR20A (Protein-RNA), MIRLET7A1 (Protein-RNA), MOV10 (Affinity Capture-RNA), NXF1 (Affinity Capture-RNA), PARP12 (Proximity Label-MS)

Protein complexes (CORUM) (1)

Experimentally-characterized complexes this protein is a subunit of (★ = the complex contains a known drug target).

1 complexes by size:

Complex	Subunits	Members
SMN complex, U7 snRNA specific	7	SNRPB, SNRPD3, SNRPE, SNRPF, SNRPG, LSM10, LSM11

Disease & clinical

Genetic variants

Variant evidence for LSM10: 20 ClinVar records (0 pathogenic / likely pathogenic); 2 GWAS associations.

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	17
Likely benign	0
Benign	0

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 23 predictions of 368):

Position(s)	Effect	Δscore	Sites
1:36397777	donor_gain	1.0000
1:36397788	donor_gain	1.0000
1:36397681–36397682	donor_gain	0.9900	2
1:36397781–36397782	donor_gain	0.9900	2
1:36397789	donor_gain	0.9900
1:36394154–36394155	acceptor_loss	0.9600	6
1:36397762	donor_loss	0.9500	2
1:36397765–36397766	donor_loss	0.9500	6
1:36394156	acceptor_loss	0.9400
1:36397762	donor_loss	0.9400

AlphaMissense

279 missense substitutions predicted likely pathogenic (of 804 scored), across 76 residues. Top 20 hotspot residues, ranked by the number of likely-pathogenic substitutions (of those reachable by a single-nucleotide change), then by mean score:

Residue	Likely-pathogenic substitutions	Mean am_pathogenicity	Max am_pathogenicity
D47	8	0.936	0.976
N51	8	0.921	0.984
N15	8	0.821	0.895
H83	8	0.724	0.908
F73	7	0.915	0.977
M50	7	0.903	0.991
F49	7	0.897	0.985
E9	7	0.843	0.923
D35	6	0.830	0.876
D61	6	0.811	0.874
P85	6	0.753	0.864
V31	6	0.749	0.976
D32	6	0.706	0.821
G64	6	0.660	0.838
G41	5	0.958	0.985
S16	5	0.925	0.971
V79	5	0.869	0.988
S37	5	0.857	0.957
V82	5	0.854	0.992
G76	5	0.850	0.967

HPA cancer prognostics

RNA cancer specificity: Low cancer specificity

Human Protein Atlas survival analysis — favorable = higher expression predicts better survival.

2 prognostic cancer types:

Cancer	Prognostic	p-value
Liver Hepatocellular Carcinoma (TCGA)	unfavorable	1.73e-06
Kidney Chromophobe (TCGA)	unfavorable	0.000137

Disease associations

OMIM: gene MIM:617909 | disease phenotypes:

GWAS associations

2 associations:

Study	Trait	p-value
GCST005974_10	Neutrophil count	4e-16
GCST008256_6	Diverticulitis	2e-6

EFO canonical traits (from GWAS)

1 canonical traits:

EFO ID	Trait name
EFO:0004833	neutrophil count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (CPIC guideline: no)

CTD chemical–gene interactions

29 total (human), top 29 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	increases methylation, increases expression	2
aristolochic acid I	increases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	affects expression	1
arsenite	affects binding, increases reaction	1
sodium arsenite	decreases expression	1
potassium chromate(VI)	decreases expression, affects cotreatment	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
di-n-butylphosphoric acid	affects expression	1
ICG 001	increases expression	1
(4-amino-1,4-dihydro-3-(2-pyridyl)-5-thioxo-1,2,4-triazole)copper(II)	decreases expression	1
2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidine	decreases expression, increases response to substance	1
jinfukang	increases expression	1
Resveratrol	affects cotreatment, increases expression	1
Air Pollutants	decreases expression, increases abundance	1
Arsenic	affects methylation	1
Vehicle Emissions	decreases expression, increases abundance	1
Formaldehyde	decreases expression	1
Methyl Methanesulfonate	decreases expression	1
Nickel	increases expression	1
Plant Extracts	affects cotreatment, increases expression	1
Smoke	decreases expression	1
Thiram	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Aflatoxin B1	increases expression	1
Asbestos, Crocidolite	increases expression	1
Sodium Selenite	increases expression	1
Copper Sulfate	decreases expression	1
Particulate Matter	decreases expression, increases abundance	1

Clinical trials (associated diseases)

Via MONDO — disease-level, not drug-specific.