Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	27257
Gene name	LSM1 homolog, mRNA degradation associated
Gene symbol	LSM1
Synonyms (NCBI Gene)	CASMFICUSYJL124C
Chromosome	8
Chromosome location	8p11.23
Summary	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. Inc

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miRTarBase ID	miRNA	Experiments	Reference
MIRT028662	hsa-miR-30a-5p	Proteomics	18668040
MIRT030039	hsa-miR-26b-5p	Microarray	19088304
MIRT459086	hsa-miR-128-3p	PAR-CLIP	23592263
MIRT459085	hsa-miR-216a-3p	PAR-CLIP	23592263
MIRT459084	hsa-miR-3681-3p	PAR-CLIP	23592263
MIRT459083	hsa-miR-1252-5p	PAR-CLIP	23592263
MIRT459082	hsa-miR-4252	PAR-CLIP	23592263
MIRT459081	hsa-miR-4294	PAR-CLIP	23592263
MIRT459080	hsa-miR-1227-3p	PAR-CLIP	23592263
MIRT459079	hsa-miR-3064-3p	PAR-CLIP	23592263
MIRT459078	hsa-miR-3611	PAR-CLIP	23592263
MIRT459077	hsa-miR-6818-5p	PAR-CLIP	23592263
MIRT459086	hsa-miR-128-3p	PAR-CLIP	23592263
MIRT459085	hsa-miR-216a-3p	PAR-CLIP	23592263
MIRT459084	hsa-miR-3681-3p	PAR-CLIP	23592263
MIRT459083	hsa-miR-1252-5p	PAR-CLIP	23592263
MIRT459082	hsa-miR-4252	PAR-CLIP	23592263
MIRT459081	hsa-miR-4294	PAR-CLIP	23592263
MIRT459080	hsa-miR-1227-3p	PAR-CLIP	23592263
MIRT459079	hsa-miR-3064-3p	PAR-CLIP	23592263
MIRT459078	hsa-miR-3611	PAR-CLIP	23592263
MIRT459077	hsa-miR-6818-5p	PAR-CLIP	23592263
MIRT2034396	hsa-miR-1244	CLIP-seq
MIRT2034397	hsa-miR-1323	CLIP-seq
MIRT2034398	hsa-miR-139-5p	CLIP-seq
MIRT2034399	hsa-miR-142-5p	CLIP-seq
MIRT2034400	hsa-miR-186	CLIP-seq
MIRT2034401	hsa-miR-3122	CLIP-seq
MIRT2034402	hsa-miR-3133	CLIP-seq
MIRT2034403	hsa-miR-3185	CLIP-seq
MIRT2034404	hsa-miR-3201	CLIP-seq
MIRT2034405	hsa-miR-338-5p	CLIP-seq
MIRT2034406	hsa-miR-340	CLIP-seq
MIRT2034407	hsa-miR-3913-5p	CLIP-seq
MIRT2034408	hsa-miR-450b-3p	CLIP-seq
MIRT2034409	hsa-miR-4677-3p	CLIP-seq
MIRT2034410	hsa-miR-4679	CLIP-seq
MIRT2034411	hsa-miR-4703-3p	CLIP-seq
MIRT2034412	hsa-miR-4735-5p	CLIP-seq
MIRT2034413	hsa-miR-4791	CLIP-seq
MIRT2034414	hsa-miR-548o	CLIP-seq
MIRT2034415	hsa-miR-618	CLIP-seq
MIRT2034416	hsa-miR-622	CLIP-seq
MIRT2034417	hsa-miR-769-3p	CLIP-seq
MIRT2563896	hsa-miR-1208	CLIP-seq
MIRT2563897	hsa-miR-1227	CLIP-seq
MIRT2034396	hsa-miR-1244	CLIP-seq
MIRT2563898	hsa-miR-1252	CLIP-seq
MIRT2563899	hsa-miR-128	CLIP-seq
MIRT2563900	hsa-miR-138	CLIP-seq
MIRT2034399	hsa-miR-142-5p	CLIP-seq
MIRT2034400	hsa-miR-186	CLIP-seq
MIRT2563901	hsa-miR-30a	CLIP-seq
MIRT2563902	hsa-miR-30b	CLIP-seq
MIRT2563903	hsa-miR-30c	CLIP-seq
MIRT2563904	hsa-miR-30d	CLIP-seq
MIRT2563905	hsa-miR-30e	CLIP-seq
MIRT2034401	hsa-miR-3122	CLIP-seq
MIRT2034402	hsa-miR-3133	CLIP-seq
MIRT2034403	hsa-miR-3185	CLIP-seq
MIRT2034404	hsa-miR-3201	CLIP-seq
MIRT2034405	hsa-miR-338-5p	CLIP-seq
MIRT2563906	hsa-miR-339-5p	CLIP-seq
MIRT2034406	hsa-miR-340	CLIP-seq
MIRT2563907	hsa-miR-3607-3p	CLIP-seq
MIRT2034407	hsa-miR-3913-5p	CLIP-seq
MIRT2563908	hsa-miR-4477a	CLIP-seq
MIRT2034408	hsa-miR-450b-3p	CLIP-seq
MIRT2563909	hsa-miR-452	CLIP-seq
MIRT2563910	hsa-miR-4676-3p	CLIP-seq
MIRT2034411	hsa-miR-4703-3p	CLIP-seq
MIRT2034412	hsa-miR-4735-5p	CLIP-seq
MIRT2034413	hsa-miR-4791	CLIP-seq
MIRT2563911	hsa-miR-548ac	CLIP-seq
MIRT2563912	hsa-miR-548d-3p	CLIP-seq
MIRT2563913	hsa-miR-548q	CLIP-seq
MIRT2563914	hsa-miR-548z	CLIP-seq
MIRT2034415	hsa-miR-618	CLIP-seq
MIRT2034417	hsa-miR-769-3p	CLIP-seq
MIRT2563896	hsa-miR-1208	CLIP-seq
MIRT2563897	hsa-miR-1227	CLIP-seq
MIRT2034396	hsa-miR-1244	CLIP-seq
MIRT2563898	hsa-miR-1252	CLIP-seq
MIRT2563899	hsa-miR-128	CLIP-seq
MIRT2563900	hsa-miR-138	CLIP-seq
MIRT2034399	hsa-miR-142-5p	CLIP-seq
MIRT2034400	hsa-miR-186	CLIP-seq
MIRT2563901	hsa-miR-30a	CLIP-seq
MIRT2563902	hsa-miR-30b	CLIP-seq
MIRT2563903	hsa-miR-30c	CLIP-seq
MIRT2563904	hsa-miR-30d	CLIP-seq
MIRT2563905	hsa-miR-30e	CLIP-seq
MIRT2034401	hsa-miR-3122	CLIP-seq
MIRT2034402	hsa-miR-3133	CLIP-seq
MIRT2034403	hsa-miR-3185	CLIP-seq
MIRT2034404	hsa-miR-3201	CLIP-seq
MIRT2034405	hsa-miR-338-5p	CLIP-seq
MIRT2563906	hsa-miR-339-5p	CLIP-seq
MIRT2034406	hsa-miR-340	CLIP-seq
MIRT2563907	hsa-miR-3607-3p	CLIP-seq
MIRT2034407	hsa-miR-3913-5p	CLIP-seq
MIRT2563908	hsa-miR-4477a	CLIP-seq
MIRT2034408	hsa-miR-450b-3p	CLIP-seq
MIRT2563909	hsa-miR-452	CLIP-seq
MIRT2563910	hsa-miR-4676-3p	CLIP-seq
MIRT2034411	hsa-miR-4703-3p	CLIP-seq
MIRT2034412	hsa-miR-4735-5p	CLIP-seq
MIRT2034413	hsa-miR-4791	CLIP-seq
MIRT2563913	hsa-miR-548q	CLIP-seq
MIRT2034415	hsa-miR-618	CLIP-seq
MIRT2034417	hsa-miR-769-3p	CLIP-seq

Show/Hide all (24)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000290	Process	Deadenylation-dependent decapping of nuclear-transcribed mRNA	IBA
GO:0000375	Process	RNA splicing, via transesterification reactions	TAS	10369684
GO:0000932	Component	P-body	IBA
GO:0000932	Component	P-body	IEA
GO:0000956	Process	Nuclear-transcribed mRNA catabolic process	IEA
GO:0003723	Function	RNA binding	HDA	22658674, 22681889
GO:0003723	Function	RNA binding	IEA
GO:0003729	Function	MRNA binding	IBA
GO:0005515	Function	Protein binding	IPI	14667819, 15231747, 18172165, 19628699, 20584987, 20852261, 25416956, 26871637, 28514442, 32296183, 32814053, 33961781
GO:0005634	Component	Nucleus	IDA	18559850
GO:0005634	Component	Nucleus	TAS	10369684
GO:0005737	Component	Cytoplasm	IDA	18559850
GO:0005737	Component	Cytoplasm	IEA
GO:0005829	Component	Cytosol	TAS
GO:0006397	Process	MRNA processing	IEA
GO:0006397	Process	MRNA processing	TAS	10369684
GO:0008380	Process	RNA splicing	IEA
GO:0008380	Process	RNA splicing	TAS	10369684
GO:0019827	Process	Stem cell population maintenance	IEA
GO:0030182	Process	Neuron differentiation	IEA
GO:0045665	Process	Negative regulation of neuron differentiation	IEA
GO:0071044	Process	Histone mRNA catabolic process	IMP	18172165
GO:1990726	Component	Lsm1-7-Pat1 complex	IBA
GO:1990904	Component	Ribonucleoprotein complex	IEA

MIM	HGNC	e!Ensembl
607281	20472	ENSG00000175324

O15116

Protein name

U6 snRNA-associated Sm-like protein LSm1 (Cancer-associated Sm-like) (Small nuclear ribonuclear CaSm)

Protein function

Plays a role in the degradation of histone mRNAs, the only eukaryotic mRNAs that are not polyadenylated (PubMed:18172165). Probably also part of an LSm subunits-containing complex involved in the general process of mRNA degradation (By similarit

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF01423	LSM	8 → 76	LSM domain	Domain

Sequence

MNYMPGTASLIEDIDKKHLVLLRDGRTLIGFLRSIDQFANLVLHQTVERIHVGKKYGDIP
RGIFVVRGENVVLLGEIDLEKESDTPLQQVSIEEILEEQRVEQQTKLEAEKLKVQALKDR
GLSIPRADTLDEY

Sequence length

133

Interactions

View interactions

	KEGG		Reactome
	RNA degradation		mRNA decay by 5' to 3' exoribonuclease

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Causal Diseases (2)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
FICUS syndrome	Likely pathogenic; Pathogenic	rs2130643543	RCV005410947	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Global developmental delay	Likely pathogenic; Pathogenic	rs2130643543	RCV002254144	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (10)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
BICUSPID AORTIC VALVE	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Complex neurodevelopmental disorder	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL HEMIVERTEBRA	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CRYPTORCHIDISM	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INTELLECTUAL DISABILITY	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NON-SPECIFIC SYNDROMIC INTELLECTUAL DISABILITY	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PATENT DUCTUS ARTERIOSUS AFTER PREMATURE BIRTH	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PENILE HYPOSPADIAS	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCHIZOPHRENIA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
STRABISMUS	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (18)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Breast Carcinoma	Breast Carcinoma	BEFREE	17001308, 21788678		★★★★★ ★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	17001308, 20940404, 35692083, 37995895	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma of lung	Lung carcinoma	BEFREE	18218995		★★★★★ ★☆☆☆☆ Found in Text Mining only
Epilepsy	Epilepsy	Pubtator	40658715	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	BEFREE	17001308, 21788678		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of lung	Lung Cancer	BEFREE	18218995		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of pancreas	Pancreatic cancer	BEFREE	12894573		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of prostate	Prostate cancer	BEFREE	11953827		★★★★★ ★☆☆☆☆ Found in Text Mining only
Mammary Neoplasms	Mammary Neoplasms	LHGDN	17001308		★★★★★ ★☆☆☆☆ Found in Text Mining only
Mesothelioma	Mesothelioma	BEFREE	18218995		★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	16024624, 16549328, 26905262		★★★★★ ★☆☆☆☆ Found in Text Mining only
Pancreatic carcinoma	Pancreatic carcinoma	BEFREE	12894573		★★★★★ ★☆☆☆☆ Found in Text Mining only
Pancreatic Neoplasm	Pancreatic Neoplasm	BEFREE	11490361, 9230209		★★★★★ ★☆☆☆☆ Found in Text Mining only
Prostate carcinoma	Prostate cancer	BEFREE	11953827		★★★★★ ★☆☆☆☆ Found in Text Mining only
Prostatic Neoplasms	Prostatic Neoplasms	LHGDN	11953827		★★★★★ ★☆☆☆☆ Found in Text Mining only
Schizophrenia	Schizophrenia	GWASCAT_DG	22037555, 28991256		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Schizophrenia	Schizophrenia	GWASDB_DG	22037555		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Schizophrenia	Schizophrenia	Pubtator	22037555	Associate	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

LSM1 (LSM1 homolog, mRNA degradation associated)