LSM6

LSM6 homolog, U6 small nuclear RNA and mRNA degradation associated, the group of LSm proteins

Basic information

Region (hg38): 4:146175702-146200000

Links

ENSG00000164167 ∙ NCBI:11157 ∙ OMIM:607286 ∙ HGNC:17017 ∙ Uniprot:P62312 ∙ 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 LSM6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LSM6 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			2			2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	2	0	0

Variants in LSM6

This is a list of pathogenic ClinVar variants found in the LSM6 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-146182927-T-G		not specified	Uncertain significance (Sep 14, 2023)
4-146187382-A-G		not specified	Uncertain significance (Sep 22, 2023)
4-146189651-A-T		not specified	Uncertain significance (May 20, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LSM6	protein_coding	protein_coding	ENST00000502781	3	24316

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.873	0.126	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.54	16	45.1	0.355	0.00000251	512
Missense in Polyphen		6	12.018	0.49923		167
Synonymous	-0.0125	16	15.9	1.00	7.53e-7	148
Loss of Function	2.40	0	6.73	0.00	5.37e-7	54

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

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). Component of LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner, facilitating the efficient association of RNA processing factors with their substrates. Component of the cytoplasmic LSM1- LSM7 complex, which is thought to be involved in mRNA degradation by activating the decapping step in the 5'-to-3' mRNA decay pathway (Probable). {ECO:0000269|PubMed:10523320, ECO:0000269|PubMed:28781166, ECO:0000305|PubMed:12515382}.
• 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: 0.124

Intolerance Scores

• rvis_EVS: 0.1
• rvis_percentile_EVS: 60.96

Haploinsufficiency Scores

• pHI: 0.906
• hipred: Y
• hipred_score: 0.833
• ghis: 0.699

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.683

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lsm6

Gene ontology

• Biological process: mRNA splicing, via spliceosome;tRNA processing;RNA splicing;maturation of SSU-rRNA;exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay
• Cellular component: P-body;nucleus;nucleoplasm;U6 snRNP;nucleolus;cytosol;small nuclear ribonucleoprotein complex;U4/U6 x U5 tri-snRNP complex;U2-type precatalytic spliceosome;Lsm2-8 complex
• Molecular function: RNA binding;protein binding