LSM3

LSM3 homolog, U6 small nuclear RNA and mRNA degradation associated, the group of LSm proteins

Basic information

Region (hg38): 3:14178817-14201122

Links

ENSG00000170860 ∙ NCBI:27258 ∙ OMIM:607283 ∙ HGNC:17874 ∙ Uniprot:P62310 ∙ 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 LSM3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LSM3 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					1	1
missense			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1	1	2
Total	0	0	7	1	2

Variants in LSM3

This is a list of pathogenic ClinVar variants found in the LSM3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
3-14178880-A-T		not specified	Uncertain significance (Apr 20, 2023)
3-14178939-C-T			Benign/Likely benign (Oct 28, 2024)
3-14179017-C-G			Benign (Feb 11, 2019)
3-14181574-C-T			Benign (Mar 29, 2018)
3-14181599-A-T		not specified	Uncertain significance (May 23, 2024)
3-14183960-G-A		not specified	Uncertain significance (Aug 19, 2024)
3-14198066-G-C		not specified	Uncertain significance (Jun 28, 2023)
3-14198069-C-T		not specified	Uncertain significance (Oct 16, 2024)
3-14198076-A-T		not specified	Uncertain significance (Feb 19, 2025)
3-14198109-T-C		not specified	Uncertain significance (Oct 05, 2022)
3-14198111-G-A		not specified	Uncertain significance (Nov 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LSM3	protein_coding	protein_coding	ENST00000306024	4	22762

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000395	0.221	125711	0	36	125747	0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.397	50	58.6	0.854	0.00000316	657
Missense in Polyphen		9	11.973	0.75168		172
Synonymous	0.0385	21	21.2	0.989	0.00000108	198
Loss of Function	-0.136	8	7.59	1.05	5.57e-7	72

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000244	0.000242
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.000221	0.000220
Middle Eastern	0.000109	0.000109
South Asian	0.0000327	0.0000327
Other	0.000163	0.000163

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);Metabolism of RNA;mRNA Splicing - Major Pathway;mRNA decay by 5, to 3, exoribonuclease;Deadenylation-dependent mRNA decay;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.156

Intolerance Scores

• loftool: 0.673
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.25

Haploinsufficiency Scores

• pHI: 0.140
• hipred: Y
• hipred_score: 0.769
• ghis: 0.691

Essentials

• essential_gene_CRISPR: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.990

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Lsm3
• Phenotype: immune system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); homeostasis/metabolism phenotype

Gene ontology

• Biological process: mRNA splicing, via spliceosome;mRNA processing;cytoplasmic mRNA processing body assembly;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