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.

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.

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				5	1	6
missense			28	1		29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	28	6	1

Variants in LSM11

This is a list of pathogenic ClinVar variants found in the LSM11 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-157743760-C-T		not specified	Uncertain significance (Mar 11, 2022)
5-157743767-G-A		not specified	Uncertain significance (Apr 13, 2022)
5-157743767-G-C		not specified	Uncertain significance (Jan 09, 2024)
5-157743768-G-C			Likely benign (Sep 01, 2022)
5-157743773-C-T		not specified	Uncertain significance (Nov 02, 2023)
5-157743779-C-G		not specified	Uncertain significance (Aug 15, 2023)
5-157743800-C-G		not specified	Uncertain significance (Nov 18, 2022)
5-157743858-C-T			Likely benign (Jan 01, 2023)
5-157743895-A-G		not specified	Uncertain significance (Oct 20, 2023)
5-157743920-C-A		not specified	Uncertain significance (May 23, 2023)
5-157743956-G-A		not specified	Uncertain significance (Dec 01, 2022)
5-157743958-G-A		LSM11-related disorder	Likely benign (May 23, 2022)
5-157743978-G-A		not specified	Benign (Jan 24, 2024)
5-157743992-C-G		not specified	Uncertain significance (May 11, 2022)
5-157744004-G-T		not specified	Uncertain significance (Aug 30, 2022)
5-157744006-G-A		not specified	Uncertain significance (Mar 31, 2024)
5-157744018-C-A		not specified	Uncertain significance (Dec 14, 2021)
5-157744032-C-T			Likely benign (Jul 01, 2024)
5-157744039-C-G		not specified	Uncertain significance (Dec 18, 2023)
5-157744055-C-G		not specified	Uncertain significance (Sep 14, 2022)
5-157744061-C-G		not specified	Uncertain significance (Jan 27, 2022)
5-157744067-A-C		not specified	Uncertain significance (Dec 02, 2021)
5-157744073-A-C		not specified	Uncertain significance (Dec 02, 2021)
5-157744075-C-T		not specified	Uncertain significance (Feb 06, 2023)
5-157744154-G-C		not specified	Uncertain significance (Jun 07, 2024)

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