LSM2

LSM2 homolog, U6 small nuclear RNA and mRNA degradation associated, the group of LSm proteins

Basic information

Region (hg38): 6:31797396-31806966

Previous symbols: [ "C6orf28" ]

Links

ENSG00000204392 ∙ NCBI:57819 ∙ OMIM:607282 ∙ HGNC:13940 ∙ Uniprot:Q9Y333 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LSM2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LSM2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	0	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LSM2	protein_coding	protein_coding	ENST00000375661	5	9589

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000240	0.316	123436	0	14	123450	0.0000567

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.83	14	50.5	0.277	0.00000260	610
Missense in Polyphen		3	12.931	0.232		151
Synonymous	0.805	17	21.8	0.781	0.00000124	181
Loss of Function	0.0218	7	7.06	0.991	3.84e-7	78

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000664	0.0000658
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000559	0.0000547
Finnish	0.0000480	0.0000462
European (Non-Finnish)	0.0000653	0.0000631
Middle Eastern	0.0000559	0.0000547
South Asian	0.0000988	0.0000988
Other	0.000174	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays 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 binds specifically to the 3'-terminal U-tract of U6 snRNA (PubMed:10523320). {ECO:0000269|PubMed:10523320, ECO:0000269|PubMed:28781166}.
• Pathway: RNA degradation - Homo sapiens (human);Spliceosome - Homo sapiens (human);mRNA Processing;Metabolism of RNA;mRNA Splicing - Major Pathway;mRNA decay by 5, to 3, exoribonuclease;Deadenylation-dependent mRNA decay;mRNA Splicing - Minor Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.118

Intolerance Scores

• loftool: 0.677
• rvis_EVS: 0.19
• rvis_percentile_EVS: 66.32

Haploinsufficiency Scores

• pHI: 0.496
• hipred: Y
• hipred_score: 0.796
• ghis: 0.587

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.731

Mouse Genome Informatics

• Gene name: Lsm2

Gene ontology

• Biological process: mRNA splicing, via spliceosome;exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay
• Cellular component: P-body;nucleus;nucleoplasm;U6 snRNP;cytosol;U4/U6 x U5 tri-snRNP complex;U2-type precatalytic spliceosome;catalytic step 2 spliceosome;Lsm2-8 complex;Lsm1-7-Pat1 complex
• Molecular function: RNA binding;protein binding;U6 snRNA binding;Ral GTPase binding