LSM7 (LSM7 homolog, U6 small nuclear RNA and mRNA degradation associated)

Gene

• Entrez ID: 51690
• Gene name: LSM7 homolog, U6 small nuclear RNA and mRNA degradation associated
• Gene symbol: LSM7
• Synonyms (NCBI Gene): LDCA, YNL147W
• Chromosome: 19
• Chromosome location: 19p13.3
• Summary: 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

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT049616	hsa-miR-92a-3p	CLASH	23622248
MIRT2390386	hsa-miR-3173-5p	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000398	Process	MRNA splicing, via spliceosome	IDA	28781166
GO:0000398	Process	MRNA splicing, via spliceosome	IEA
GO:0000398	Process	MRNA splicing, via spliceosome	NAS	30975767
GO:0000956	Process	Nuclear-transcribed mRNA catabolic process	IEA
GO:0003723	Function	RNA binding	IBA
GO:0003723	Function	RNA binding	IEA
GO:0005515	Function	Protein binding	IPI	12165861, 14603251, 14667819, 15231747, 19628699, 21988832, 22365833, 25416956, 28514442, 31515488, 32296183, 33961781, 35271311
GO:0005634	Component	Nucleus	IDA	26912367
GO:0005634	Component	Nucleus	IEA
GO:0005634	Component	Nucleus	NAS	30975767
GO:0005654	Component	Nucleoplasm	TAS
GO:0005681	Component	Spliceosomal complex	IEA
GO:0005681	Component	Spliceosomal complex	IPI	30975767
GO:0005688	Component	U6 snRNP	IBA
GO:0005689	Component	U12-type spliceosomal complex	IBA
GO:0005829	Component	Cytosol	TAS
GO:0006397	Process	MRNA processing	IEA
GO:0008380	Process	RNA splicing	IEA
GO:0017070	Function	U6 snRNA binding	NAS	10523320
GO:0046540	Component	U4/U6 x U5 tri-snRNP complex	IDA	26912367
GO:0046540	Component	U4/U6 x U5 tri-snRNP complex	IPI	30975767
GO:0071004	Component	U2-type prespliceosome	IBA
GO:0071005	Component	U2-type precatalytic spliceosome	IDA	28781166
GO:0071013	Component	Catalytic step 2 spliceosome	IBA
GO:0097526	Component	Spliceosomal tri-snRNP complex	IBA
GO:0120115	Component	Lsm2-8 complex	IDA	10523320
GO:1990726	Component	Lsm1-7-Pat1 complex	IBA
GO:1990904	Component	Ribonucleoprotein complex	IEA

Other IDs

• MIM: 607287
• HGNC: 20470
• e!Ensembl: ENSG00000130332

Protein

• UniProt ID: Q9UK45
• Protein name: U6 snRNA-associated Sm-like protein LSm7
• Protein 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) (PubMed:28781166). The heptameric LSM2-8 complex
• PDB: 3JCR, 5O9Z, 6AH0, 6AHD, 6QW6, 6QX9, 7ABG, 8H6E, 8H6J, 8H6K, 8H6L, 8QO9, 8QXD, 8QZS, 8R08, 8R09, 8R0A, 8R0B, 8RM5
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF01423	LSM	13 → 86	LSM domain	Domain

• Sequence:

  MADKEKKKKESILDLSKYIDKTIRVKFQGGREASGILKGFDPLLNLVLDGTIEYMRDPDD
  QYKLTEDTRQLGLVVCRGTSVVLICPQDGMEAIPNPFIQQQDA

• Sequence length: 103

Pathways

KEGG:

RNA degradation
Spliceosome

Reactome:

mRNA decay by 5' to 3' exoribonuclease
mRNA Splicing - Major Pathway

Associated diseases

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)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
In utero death	Likely pathogenic	rs753556902	RCV001543593	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Joubert syndrome 36	Likely pathogenic	rs753556902	RCV005861229	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Leukodystrophy	Pathogenic	rs750219615	RCV001543592	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
LSM7-related leukodystrophy and cerebellar atrophy	Pathogenic	rs750219615	RCV005409794	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Malignant Neoplasms	Malignant Neoplasm	BEFREE	16360390		★☆☆☆☆ Found in Text Mining only