LSM11

LSM11, U7 small nuclear RNA associated, the group of LSm proteins

Basic information

Region (hg38): 5:157743712-157760709

Links

ENSG00000155858

∙ NCBI:134353 ∙ OMIM:617910 ∙ HGNC:30860 ∙ Uniprot:P83369 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

Tourette syndrome (No Known Disease Relationship), mode of inheritance: Unknown
Aicardi-Goutieres syndrome 8 (Limited), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LSM11 gene.

not_specified (60 variants)
not_provided (10 variants)
LSM11-related_disorder (2 variants)
Aicardi-Goutieres_syndrome_8 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LSM11 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000173491.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	8 clinvar		9
missense	1 clinvar		59 clinvar	1 clinvar		61
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	1	0	60	9	0

Highest pathogenic variant AF is 0.00000210783

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LSM11	protein_coding	protein_coding	ENST00000286307	4	17015

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.604	0.394	125743	0	4	125747	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.881	152	186	0.818	0.0000107	2220
Missense in Polyphen		40	53.494	0.74774		598
Synonymous	0.615	67	73.7	0.909	0.00000375	817
Loss of Function	2.60	2	11.5	0.174	7.14e-7	130

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000724	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00000976	0.00000879
Middle Eastern	0.0000724	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Component of the U7 snRNP complex that is involved in the histone 3'-end pre-mRNA processing (By similarity). Increases U7 snRNA levels but not histone 3'-end pre-mRNA processing activity, when overexpressed. Required for cell cycle progression from G1 to S phases. Binds specifically to the Sm-binding site of U7 snRNA. {ECO:0000250, ECO:0000269|PubMed:16914750}.;
Pathway: Gene expression (Transcription);RNA Polymerase II Transcription;SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs;Metabolism of RNA;Processing of Capped Intronless Pre-mRNA;Cleavage of Growing Transcript in the Termination Region ;RNA Polymerase II Transcription Termination;SLBP independent Processing of Histone Pre-mRNAs (Consensus)

Recessive Scores

pRec: 0.113

Haploinsufficiency Scores

pHI: 0.279
hipred: Y
hipred_score: 0.739
ghis: 0.600

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: E
essential_gene_gene_trap: E
gene_indispensability_pred: E
gene_indispensability_score: 0.893

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Lsm11
Phenotype: hematopoietic system phenotype;

Gene ontology

Biological process: termination of RNA polymerase II transcription;mRNA 3'-end processing by stem-loop binding and cleavage;histone mRNA metabolic process;positive regulation of G1/S transition of mitotic cell cycle
Cellular component: nucleus;nucleoplasm;U7 snRNP;telomerase holoenzyme complex;nuclear body;histone pre-mRNA 3'end processing complex
Molecular function: protein binding;U7 snRNA binding