LSM8

LSM8 homolog, U6 small nuclear RNA associated, the group of LSm proteins

Basic information

Region (hg38): 7:118184143-118204035

Links

ENSG00000128534 ∙ NCBI:51691 ∙ OMIM:607288 ∙ HGNC:20471 ∙ Uniprot:O95777 ∙ 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 LSM8 gene.

• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LSM8 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						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	1

Variants in LSM8

This is a list of pathogenic ClinVar variants found in the LSM8 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-118188313-G-A			Benign (Dec 28, 2017)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LSM8	protein_coding	protein_coding	ENST00000249299	4	8793

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00512	0.718	125726	0	9	125735	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.09	29	50.8	0.570	0.00000254	611
Missense in Polyphen		5	13.569	0.36849		200
Synonymous	-0.464	22	19.4	1.13	0.00000108	186
Loss of Function	0.748	4	5.97	0.670	3.55e-7	66

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000298	0.0000298
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000528	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000164	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 Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.130

Haploinsufficiency Scores

• pHI: 0.150
• ghis: 0.700

Essentials

• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.683

Mouse Genome Informatics

• Gene name: Lsm8

Zebrafish Information Network

• Gene name: lsm8
• Affected structure: thymus
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: mRNA splicing, via spliceosome;RNA metabolic process
• Cellular component: nucleus;nucleoplasm;U6 snRNP;U4/U6 x U5 tri-snRNP complex;U2-type precatalytic spliceosome;Lsm2-8 complex
• Molecular function: RNA binding;protein binding;U6 snRNA binding