LSM11

protein-coding

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

Gene summary

Enables U7 snRNA binding activity. Involved in mRNA 3'-end processing by stem-loop binding activity and cleavage; positive regulation of G1/S transition of mitotic cell cycle; and regulation of chromatin organization. Located in nuclear body. Part of U7 snRNP and telomerase holoenzyme complex. Implicated in Aicardi-Goutieres syndrome. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_173491.4

Inheritance

ClinVar variants

P:1U:73B:15

Top phenotype

LSM11-related disorder

gnomAD constraint

pLI —, LoF o/e 0.17

Max pathogenic AF

—

Genomic locus

chr5:157,743,712-157,760,709

External References & Databases

Ensembl (ENSG00000155858)

Transcript & Mutation Effects

hg38 • Region Span ~17.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

Aicardi-Goutieres syndrome 8LIMITED

Inheritance Pattern: Unknown

Disease ID:MONDO:0030361

Submitter: Labcorp Genetics (formerly Invitae)

Aicardi-Goutieres syndrome 8LIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0030361

Submitter: PanelApp Australia

Tourette syndromeNO_KNOWN

Inheritance Pattern: Unknown

Disease ID:MONDO:0007661

Submitter: Labcorp Genetics (formerly Invitae)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to LSM11 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 74

not providedTotal: 15

LSM11-related disorderTotal: 2

Aicardi-Goutieres syndrome 8Total: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_173491.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	12 clinvar		13
missense	1 clinvar		70 clinvar	3 clinvar		74
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	1	0	73	15	0	89

Highest pathogenic variant AF is 0.000002107834

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 3 of 3 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_173491.4	RefSeq	NP_775762.1	4	MANE Select
ENST00000286307.6	Ensembl	ENSP00000286307.5	4	MANE Select
ENST00001134300.1	Ensembl	ENSP00000804615.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

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

Molecular Function

protein binding
U7 snRNA binding

Cellular Component

nucleus
nucleoplasm
U7 snRNP
telomerase holoenzyme complex
nuclear body

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000286307
Coding exons: 4
Length: 17015
Individuals with no LoFs: 125743
Homozygous LoFs: 0
Heterozygous LoFs: 4
Defined: 125747
p: 0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.881	152	186	0.818	0.0000107	2220
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000072	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000098	0.0000088	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.113

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.893

Gene Damage Prediction

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